Arguably the best philosophical defense of atheism, in my opinion, can be found in Michael Martin's book, Atheism: A Philosophical Justification. A successful response to Martin's arguments, therefore, will go a long way in providing evidence for the rational acceptability of belief in God. In his work, Martin treats the topics of negative atheism (giving objections to theistic arguments) and positive atheism (giving affirmative reasons to justify atheism, e.g. the problem of suffering). In this post, I would like to explore Martin's reasons for rejecting the Thomistic Cosmological Argument (TCA)  and provide an answer to these criticisms.
Martin begins, "In this argument [the Second Way] Aquinas attempts to show that there could not be an infinite series of efficient causes and consequently there must be a first cause. . . . An efficient cause of something, for Aristotle and Aquinas, is not a prior event but a substantial agent that brings about change." 
Martin is correct to point out that efficient causality is not envisaged as something that takes place in time necessarily. A house that exists from eternity still needs a foundation, even though the foundation doesn't precede the rest of the house in time. Rather, the foundation is causally prior, but not temporally prior, to the rest of the house.
Nevertheless, Martin is mistaken in saying that efficient causality has to do with change. The argument from change is Thomas' First Way, and not the Second Way. The Second Way has to do with why some thing X exists, and not why X changes. With that said, this observation is not detrimental to Martin's case, so we will continue without further comment on this point.
"[Thomas] believed that the here-and-now maintenance of the universe could not be understood in terms of an infinite causal series." 
This is a correct summation. Now onto Martin's objections:
"The first cause, even if established, need not be God . . ." 
Unfortunately for Martin, this rather swift dismissal of Thomas' conclusion completely overlooks the many additional arguments that Thomas offers in support of the first cause's possession of the divine attributes. The Five Ways are not the totality of Thomas' philosophical defense of theism. In fact, the vast majority of the Summa Theologiae in which Thomas argues specifically that the first cause is God is virtually ignored by Martin. As I have argued in my own echoing of Thomas' arguments, the first cause (Pure Being) is necessary, unique, eternal, all-present, and distinct from every other existing entity.
If Martin, or any other skeptic for that matter, is going to advance an objection that states the first cause is not God, then he will need to interact with the arguments pertinent to the establishment of the divine attributes. We will explore these in a moment.
"[A]nd Aquinas gives no non-question-begging reason why there could not be a nontemporal infinite regress of causes." 
This is one of the most common objections to the TCA. However, it's important to realize that the Summa Theologiae is literally a summary of theological and philosophical arguments. I maintain that Thomas' definitive argument against an infinite regress of causes can be found in De Ente et Essentia ("On Being and Essence"), which I summarize as follows:
1. Something exists. (Premise)
This is undoubtedly true, and Martin would agree. In order to doubt that I exist, I would first have to exist in order to doubt it.
2. Something exists only if there is such a thing as existence. (Premise)
It is at this point that Martin may simply disagree that existence is a thing at all.  Of course, existence can easily be shown to be a thing in at least one sense, even if it is not a thing in the sense that Kant meant. To illustrate, what is the difference between a real dollar bill and an imaginary one? Obviously, the essence (essence = what a thing is, its nature) of each is the same, but the real dollar bill has existence! Would Martin maintain that things can differ by a non-thing? Maybe he wouldn't go that far, but if so, I think he would simply be mistaken.
Existence is at least a thing insofar as existence is real. If existence were not real, then nothing would exist, which is patently false.
3. The essence of existence is Pure Being. (Premise)
If the essence of a dollar bill is a dollar bill (e.g. it has a specific shape, size, color, smell, etc.), then what is the essence or what-ness of existence? The essence of existence is existence itself, or what metaphysicians call Pure Being. 
4. Therefore, Pure Being exists. (Conclusion)
The argument is logically valid, and we have seen that each premise is correct, so the conclusion is likewise true: Pure Being exists. Pure Being is the first cause that Thomas alludes to in his Five Ways. In fact, even granting that there could be an infinite regress of causes, Pure Being is still needed in order to explain the existence of that regress, or of anything at all.
Now, let's consider whether Martin's objection that the first cause may not be God holds after further scrutiny. The first cause (Pure Being) must as a matter of necessity possess at least five additional qualities: necessity, unicity, eternality, omnipresence, and distinction from everything else that exists. I defend these attributes in my defense of the TCA as linked to above. Nonetheless, I will reproduce these arguments here.
Imagine a state of affairs in which nothing exists. In this case, there would be an existing state of affairs in which nothing exists, which is self-contradictory. This means that something must exist. But, since Pure Being is needed to ground the existence of anything, Pure Being must exist by necessity.
Pure Being must also be unique. For, if there were more than one Pure Being, then there would be distinctions between them. However, whatever is distinct from existence is non-existence, and because non-existent things simply do not exist, it follows that there is only one Pure Being.
Next, Pure Being is eternal and all-present. For every time and place that something exists, Pure Being must ground those times and places in which something exists. Therefore, there is no time or place in which Pure Being does not exist, so Pure Being is eternal and all-present.
Finally, Pure Being is distinct from everything else that exists. Other entities, such as a dollar bill, have an essence distinct from their existence. In short, a dollar bill is not existence itself. Now, if A is X, and B is not X, then A and B must be distinct. Hence, given that Pure Being is existence itself, and everything else is not existence itself, it follows that Pure Being is distinct from everything else.
One question about this final attribute is that if everything else is distinct from Pure Being, then how can anything else exist? The answer is that these other things do not differ from Pure Being in existence. Rather, they differ only in essence. Everything that exists does so because it participates in the single existence that there is, in Pure Being. Things differ in their essences, or natures, or what-nesses.
Of course, one could still maintain that Pure Being is not personal, etc., so that Pure Being is possibly not the God of classical theism. However, Pure Being is at least demonstrably like God.  For now, I will leave that for another discussion.
In sum, Martin has not successfully refuted the TCA, nor has he even attempted to analyze the most pertinent aspects of the Aristotelian-Thomistic metaphysical arguments for the existence of Pure Being and its divine attributes. With that said, I maintain that the TCA is a sound argument for God's existence.
 Michael Martin, Atheism: A Philosophical Justification, Temple University Press, 1990, pp. 97-100.
 ibid., p. 98.
 ibid., p. 99.
 ibid., p. 81.
 Also known as Pure Existence and Pure Actuality.
 Maybe it is something like the Hindu concept of Brahman. I don't think so, but either way, we're not left with atheism.