I don't know whether it is in deductive or deductive reasoning which has led for many Christians to be lumped with Christians that they disagree with. Perhaps it is simply because of the name, how much easier it is to presume, the way around it is to simply ask the person, to learn about the individual, yet this does not often or always occur because it takes time.
As a theist, I expect to be challenged about the existence of God or a deity, what I don't expect is for the person I'm debating with to state, "How can you persecute homosexuals?" Yes, I persecute myself.
"How can you damn people to hell?" I don't, I don't believe in hell.
"How can you vote for the Republicans?" I don't, I'm English and I've only just become eligible to vote. Furthermore, I wouldn't vote for the Tories (the British equivalent).
"You are backward and stupid." Thank you, thank you very much. If sitting with Neanderthals means I get respected, than I shall merrily walk back through the Dark Ages and beyond.
"You obviously were brainwashed." By whom? By myself? I didn't go to a faith school, my parents aren't Christians, I wasn't stalked by Christians until I gave them a chance, I didn't go to a church or Christian youth group, I didn't have any friend who tried to make me a Christian. Brainwashed indeed.
"Religion lacks reason. You're part of a religion. You lack reason." This very statement lacks reason.
"Your an idiot." Pot, kettle, grammar.
However, I do know some wonderful atheists and the wonderful atheists I know aren't the ones on the internet, they are the ones I know personally. Rather than getting incensed behind a keyboard, we can discuss with a normal amplitude ideas, beliefs, and rather than going, "HOW CAN YOU BELIEVE THAT YOU ABSOLUTE BUFFOON?!" We instead politely ask, "Why do you believe what you do?" Followed by letting the other person speak. Now, we aren't saints of debate, things can get a little heated at times and sometimes one may just want to have a big tantrum. But the point is, I don't ram a Bible down their throats, they don't ram Dawkins down mine.
Face-to-face respect happens a lot more than internet keyboard warrior respect. Ultimately, it may come down to the fact that the written word doesn't have a voice, it only has the voice which the reader gives it.