I don't think a person of faith should be president.
I'd be accused of being an anti-religious bigot, of religious intolerance, etc. But it's perfectly acceptable for Mitt Romney to say:
We need to have a person of faith lead the country.
The point being that what would be considered to be bigtory against religious people (specifically Christians, as the reporting about Keith Ellison demonstrates), is perfectly acceptable when applied to atheists. No reporter will frame this as evidence of "Romney's intolerance," just as his "commitment to his faith."
But the broader point, which Nathan goes on to make, is that it's perfectly normal and understandable that people make judgments about you based on your religious beliefs. More than that, it's absurd that given the extent to which "you gotta have faith" has become, rightly or wrongly, part of the conventional political wisdom, that passing judgments about what people actually believe or claim to believe is somehow seen as intolerant or bigoted.
If people don't want to vote for atheists that's fine. If people don't want to vote for Catholics, or Mormons, or evangelical Protestants, that's fine too. And it's fine to say it, and it's fine to say why.
Some of the motivation might be based on ignorance which veers into bigtory/racism territory - historical anti-Semitic trope, the belief that all Muslims are terrorists, etc... - but even if someone's perception of a religion is in part due to an ignorance of that religion that doesn't necessarily suggest bigotry. People are ignorant about lots of things. Ignorance is a basis for bigotry, but it isn't intrinsically bigotry.
We believe different stuff. Especially to the extent that people want to keep shoving personal religion out into our political sphere, it's important examine those differences. And if we examine those differences, we're entitled to make decisions based on them. Otherwise, the implication is that someone's religious beliefs say something incredibly important about them, but we're not actually supposed to talk about exactly what that is.