There is reason to believe that surveys conducted to identify the number of American atheists provide low estimates, but let's assume for a minute that we can trust these data as being reasonably accurate. A commonly reported number is that 1.6% of Americans identify themselves as atheists. If the U.S. population is approximately 303.5 million, this means that there are at least 4,856,000 atheists in America who identify as such. That is a lot of atheists!
Given that the number of Americans reporting no religious affiliation is 16.1%, we can assume that there are at least some people out there who are atheists but who do not want to identify themselves as atheists for a variety of reasons. As a quick example, combining the number who identify themselves as either atheist or agnostic gets us to 4% (roughly 12,140,000 people).
But the real question concerns the remaining 12% we haven't accounted for yet. Of these 12%, approximately half identify themselves as secular and without religious affiliation. How can one be secular, have no religious affiliation, and be neither atheist nor agnostic? I'm not sure, and I think a reasonable case can be made for adding them to the number we've been examining, even if only to provide a plausible upper limit. This takes us up to 10% of Americans who identify as atheist, agnostic, or secular and without any religious affiliation (approximately 30,350,000 people).
Looking at these numbers, we can conclude that are at least 4,856,000 atheists in America willing to identify themselves as atheists and that approximately 30,350,000 people, or 10% of the population, are atheists, agnostics, or secular folks.
Update: Recent survey data indicate as many as 3% of the U.S. population identify themselves as atheists.