Couldn't agree more, I'd never say anyone's smart simply because they are atheist/rationalist/etc.ist. "Stupid" is the wrong epithet too, but the most convenient one.
But yes, I do genuinely have great difficulty in crediting christians with intelligence. I deal with highly intelligent people all the time and it staggers me how many of them are christian, the concept is so blindingly obvious that I portray them as stupid just to get the kind of reaction you've seen. If atheists get this righteous, how righteous do you think christians get? To me, christianity is best summed up by Monty Python's Holy Grail crossed with the parrot sketch.
Fortunately, I know I'm right and there's no assumption involved! There is no god and I know that as sure as I know that the sun is around 150M km away, made of hydrogen and very hot. I know it as I know that rain will fall and the sea is salt. The fact that there is no god is as simple as 2 + 2.
As to tolerance, I take that from the christians themselves. What kind of monumental arrogance does it need to believe that you are the chosen one of a god and that anyone who doesn't accept your god is going to perish while you will have everlasting life? I believe that makes the level of arrogance I display very tame in comparison. Jesus and all the prophets of the bible forbid any tolerance of other, or non-religious positions - god's way or the low way. It's even one of the ten commandments for Bob's sake! Tell me why christianity, with zero tolerance of other religions, deserves anything like respect. Its adherents are free to choose their god, but they won't get any respect from me for it.
I don't even know where to begin. You cannot be positive there is no God (well, you personally can be positive, but what I mean is, you can't have proof positive) just as you can't have any proof that there is. That doesn't mean because you can't prove that there isn't that your statements are invalid, it just means that whether god exists or not is up for grabs. People say "Anything is possible" for a reason, and being skeptical doesn't mean shutting down alternate ways of thinking. It means asking for proof, and being in a position to accept that proof or refute it should there ever be an opportunity. Believers are closed-minded a lot of times. Skeptics are close-minded a lot of times. Really, everyone is so convinced their opinion is right that it's no wonder most believers really dislike skeptics and vice versa.
It makes no sense that you refuse to respect someone just because they don't respect you. It seems a silly way of looking at things. "You are intolerant of me, so I'll be intolerant of you!"