There will be an (open and out) Atheist president within my lifetime. It's becoming more and more acceptable to be Atheist or non-theist it seems. (It even seems that the majority of people in my age group, in the part of the country where I live are Atheists or non-theists who openly state that they think religion is irrelevant and I'd expect this number to grow and spread in the next few decades)
While there will still be a sizeable group of people who wouldn't vote for an Atheist (though, those same people probably wouldn't vote for any theist who is a non-Christian), the number of Atheists, Agnostics, unaffiliated, non-Christian religious, etc. in the population are growing. With more diversity, there's a greater chance that a non-Christian will be voted into office within the next few decades.
We just had our first African-American president voted in for a second term, which is something that was completely unfathomable just a short while ago. We also had our first female vice presidential candidate in a major party run for office, which is also something that was unfathomable a few decades ago. Following the tide of progress and more diversity, it's only highly likely that an Atheist will either be a serious candidate in a major party or get voted into office.
As a non-Christian religious trans person, I would vote for an Atheist. I'd also vote for a Buddhist, Muslim, Hindu, Christian, Baha'i, etc. I vote for a person's politics and character, not their religion or lack of it.