As this recent Gallup survey shows, atheists continue to be America's most unpopular minority group. Gallup asked respondents the following question:
Between now and the 2008 political conventions, there will be discussion about the qualifications of presidential candidates — their education, age, religion, race, and so on. If your party nominated a generally well-qualified person for president who happened to be [insert group name], would you vote for that person?
Fully 53% state that they would not vote a for an atheist candidate nominated by their own party, as compared to 43% who would refuse to vote for a homosexual candidate, 24% for a Mormon, 12% for a Hispanic, 11% for a woman, and single digit percentages who would refuse to support a black, Jewish, or Catholic candidate. Although the Gallup survey doesn't include these groups, Pew surveys conducted in 2005 show that 38% of Americans are categorically unwilling to support a Muslim candidate of their own party, and 15% feel the same way about an Evangelical Christian.
Some of this opposition to candidates from particular groups may be a result of using information short cuts rather than simple bigotry. For example, a survey respondent might be opposed to an atheist candidate not because he has anything against atheists as such, but because he knows that most atheists are political liberals; he doesn't want to support a candidate that is on the political left, and as a result of "rational ignorance" (discussed in my recent article here) he doesn't want to take the time to study the candidate's issue positions in detail.
Unfortunately, however, it is likely that bigotry is the main factor, even if it is not the only one. After all, the survey asks whether voters are willing to support a candidate from a particular group nominated by their own party, and the party is unlikely to nominate someone whose ideology is greatly at variance with that of the party's base. Moreover, the percentage of respondents unwilling to support a black or Jewish candidate is negligible, despite the fact that these two groups are probably even more overwhelmingly made up of liberal Democrats than are atheists. The Gallup survey also indicates that those unwilling to vote for an atheist candidate include 33% of self-identified liberals, and 52% of "moderates;" these two groups are unlikely to categorically reject an atheist candidate merely because they perceive them as liberal.
Finally, it is worth noting that the 53% figure for those unwilling to support an atheist presidential candidate of their own party is statistically indistinguishable from the 50% who, in another recent survey said they had a "mostly" or "very" unfavorable view of atheists, and the 51% who believe that "[i]t is necessary to believe in God in order to be moral and have good values" (see here). The 50% figure, by the way, is much higher than that for any other other minority group, with Muslims a distant second at a 31% "mostly" or "very" unfavorable rating.
Thus, it is likely that a high percentage of those unwilling to support an atheist candidate for the presidency even if that candidate were nominated by their own party do so because of a generalized prejudice against atheists, not because they are relying on information shortcuts.
As I have argued in the Legal Times Article linked above, and here , the widespead prejudice against atheists is in large part due to the false perception that atheism is equivalent to immorality or moral relativism. Since this post is already getting too long, I'm not going to explain in detail why this widespread view is wrong. However, for those interested, I covered that issue in the Legal Times article and in the post linked in the first part of this paragraph.