Some commenters to the post below suggested that unfavorable views of atheists may not indicate any desire to discriminate against individuals because they're atheists, but just annoyance at the views of prominent atheists (especially those who label themselves "atheist" rather than "agnostic" or "irreligious"). That's possible, and I don't know how to test this directly using existing polls, but here's the closest I could come up with.

A June 23, 1999 Fox News poll asked, "Would you consider voting for a political candidate who did not believe in God?" The responses were: Yes: 26%; No: 69%.

The closest comparable poll that I could find related to other religious groups was a Jan. 14, 2003 Fox News poll that asked, as to various groups, "Over the years there has been debate over whether a presidential candidate's religion is an obstacle or an advantage to getting elected. I'm going to read you some religious affiliations and I'd like you to tell me whether you think that affiliation is a positive thing that might make you more likely to vote for the candidate or a negative thing that might make you less likely to vote for the candidate...." Here are the results:

So in 2003, 47% of respondents said they'd ignore a candidate's being a Muslim, or see it as a plus. 49% said the candidate's being a Muslim would make it less likely that they'd vote for him, though presumably for some respondents, there would remain some possibility that they'd vote for the Muslim candidate.

Yet in 1999, only 26% of respondents said they'd consider voting "for a political candidate who doesn't believe in God" (even without any reference to the possibly emotionally laden term "atheist"), and 69% apparently wouldn't even consider such a possibility.