I look at this a bit differently than you do.  
I think that it shows that many Americans discriminate against Muslims.  
Also, I don't know it these polls question those who vote, or those who are of voting age.  It would seem to me that older, more conservative people would be more likely to have problems with a candidate who is an atheist, than would younger, less conservative people.  (I am an older person who is not at all bothered by this, but ....)
I don't understand the connection between Christianity and the two party system.