Firstly, I’d like to say that this is a stereotype created by religious individuals/groups. Secondly, I will admit stereotypes do exist for a reason. Arrogance is the key term here. Many atheists are blamed for being arrogant, but are they really? And if they are, is their behavior understandable and even justifiable?
Arrogance is found on both sides of the spectrum; the religious and the non. If a person claims to know the truth about something, they are automatically in jeopardy of being labeled as "arrogant." Divine or exclusive knowledge produces an air of arrogance as well as the claim some atheists make when they say they know there is no God, which is a non-provable, non-testable scientific claim, and is therefore an arrogant thing to say. Religionists make the claim that there is a God, which is also a non-provable, non-testable scientific claim, and is likewise an arrogant thing to say. I think the larger majority of atheists take the more rational approach to unprovable theories, though, and simply state their lack of belief in a deity. Since the larger majority of atheists (who are rationalists) don't profess to having any exceptional knowledge of God's non-existence, why are we all automatically getting the "arrogant" label from the rest of the world?
It is obvious that religion is something people take very personally, and due to its theoretical nature, it is a very touchy subject when placed under a microscope. When people make a scientific claim, such as “There IS a god,” it is only natural for other people to question it. Since religionists have no empirical evidence to support their claims and produce a reasonably acceptable answer, they view all criticism as personal attacks. Because they automatically feel threatened, they wrongly label the criticizer arrogant due to their own insecurity. I think we all know that questioning a belief does not make a person arrogant, nor does the desire for others to question their own beliefs or lack thereof. On the contrary, If anyone questions a scientist about his scientific theories, the scientist will simply answer to the best of his ability and accept criticism with open ears. This is because the objectives between the two groups of people are different. Religionists claim to already possess truth, which means there is very little reason to pursue it. Scientists do not claim this truth, and are always in pursuit of it.
And why do many atheists come across as angry? Well, if you're religious and reading this in an attempt to understand... imagine this: a world being dominated by a belief system you do not agree with or even believe is relevant to daily life, such as... everyone believes that it is virtuous to wear sneakers on Fridays. Politicians running for office will usually tack that onto their campaigns, in order to look more virtuous or "good" to the rest of their country... "I promise to lower taxes, pursue alternative energy methods, and yes... I do believe in wearing my sneakers on Friday." Can you see how irrelevant that is to being a good leader of a country? Yet the majority of people around you believe that to be a very important quality in a leader, and inherently view people who don't prioritize wearing their sneakers on Fridays as untrustworthy. After having something so obviously irrelevant force itself into all facets of life, it will wear on you, and the end result is that you'll probably have a pissed off reaction every time someone even mentions sneakers.