That ^ is irony, for the impaired among you.
First, let's talk about the idea that atheists think religious people in general are stupid. I actually think there is something to this criticism of atheists. Many don't fall into this trap, but I have come upon the meme often enough that I don't deny it is prevalent. The mistake people are making is in confusing a selective, compartmentalized rejection of rationality with stupidity. It is abundantly clear that manymany intelligent, otherwise reasonable people turn off their critical thinking when it comes to religion. I don't think this detracts from their intelligence, merely from their rationality. And yes, intelligence and rationality are often treated as synonyms, or at least closely linked, in our culture, so it's understandable that people conflate them.
In fact, if you are religious and reading this, you probably bristled when I accused you of being irrational. Generally rationality is highly prized, and you probably protested in your head that you're very rational. Perhaps you even defend your religion as a rational conclusion, pointing to various apologetics. However, if any facet of your religion requires faith, (in the "belief regardless of evidence" sense), you are rejecting rationality. I don't dispute that in every other facet of life, you may be highly rational, and I don't think you're stupid.
But when someone rejects standard methods of discovering truth, and embraces beliefs pretty much just because they feel good, it is understandable that someone who doesn't share this propensity is going to feel a gut reaction that the person is stupid, or crazy, or both. Sometimes it's hard to get beyond that gut reaction to the empirical truth that lots of intelligent people are religious.
As a thought experiment, imagine some belief you consider total, obvious codswallop - whose roots and causes are clear to you as mistakes of observation or well-known foibles of human perception. Perhaps alien abduction stories, the healing power of crystals, astrology, or bigfoot sightings. Now, don't you just have a visceral reaction along the lines of, "How could anyone believe THAT? How could someone be so blind as to what is actually going on?" If you know a believer in this stuff who is otherwise bright and sane, don't you boggle at how they can carry both of these personality aspects in the same brain? That mystified disbelief is just how your atheist friends feel about you!
The second issue here is that Christians seem to feel that atheists unfairly target them, above all other religions. Some Christians complain that we're not anti-religious, objecting to irrational beliefs whatever their form, but that we seem to be gunning for Christianity and ignoring Islam, Hinduism, Wicca, Jainism, and so on. Perhaps it's just the natural tunnel vision we're all subject to falling into. Perhaps it's that Christianity teaches a lot about how its practitioners have been persecuted. But take a step back and realize that English-speaking atheists seem to focus on Christians because that is who surrounds us! 85% of the U.S. self-identifies as Christian. Christianity is the established state religion of Britain. The people trying to inject their religious beliefs into the schools, politics, and laws of my country are certainly always Christian, in my experience. Trust me, if the Wiccans mount a campaign to teach that the Goddess gave birth to her consort the Horned God in public school science classes, we'd go after them with equal gusto. If Buddhists smugly proclaimed from campaign platforms that those without Enlightenment were obviously incapable of morality, we'd be writing invective against them too. It's nothing personal - you're the most powerful people out there right now. Sorry.