I think there are just as many arrogant and intolerant atheists out there as there are theists with the same flaws. It's just human nature sometimes and I think all kinds of people can be guilty of it. I see both sides being prejudiced and judgmental at times, but I would not want to let a few bad apples speak for the rest of the bunch.
A rude, intolerant or condescending person is going to get on my nerves no matter what their religious beliefs may or may not be. I have to do my best not to judge people, or groups of people, based on the actions and attitude of any one person. It's also important for us all to hold to whatever beliefs we value without being lulled into a sense of elitism or superiority. That goes for religious people and non-religious people alike.