I can see benefits to the principle of charity. It helps avoid flame wars, and from a Machiavellian point of view it's nice to close off the "what I actually meant was..." responses.
Some people are just bad at explaining their ideas correctly (too hasty, didn't reread themselves, not a high enough verbal SAT, foreign mother tongue, inferential distance, etc.), others are just bad at reading and understanding other's ideas correctly (too hasty, didn't read the whole argument before replying, glossed over that one word which changed the whole meaning of a sentence, etc.).
I've seen many poorly explained arguments which I could understand as true or at least pointing in interesting directions, which were summarily ignored or shot down by uncharitable readers.
The more difficult trick, at least for me, is avoiding smart people who offer stupid opinions on topics with which they are absolutely unfamiliar.
A more difficult trick yet is to notice when even smart people will offer stupid opinions on (noxious) topics, even when they are familiar with them.
I couldn't agree more to that - to a first approximation.
Now of course, the first problem is with people who think a person is either rational in general or not, right in general, or not. Being right or rational is conflated with intelligence, for people can't seem to imagine that a cognitive engine which output so many right ideas in the past could be anything but a cognitive engine which outputs right ideas in general.
For instance and in practice, I'm pretty sure I strongly disagree with some of your opinions. Yet I agree with this bit over there, and other bits as well. Isn't it baffling how some people can be so clever, so right about a huge bundle of things (read : how they have opinion so very much like mine), and then suddenly you find they believe X, where X seems incredibly stupid and wrong for obvious reasons to you.
I posit that people want to find others like them (in a continuum with finding a community of people like them, some place where they can belong), and it stings to realize that even people who hold many similar opinions still aren't carbon copies of you, that their cognitive engine doesn't work exactly the same way as yours, and that you'll have to either change yourself, or change others (both of which can be hard, unpleasant work), if you want there to be less friction between you (unless you agree to disagree, of course).
Problem number two is simply that whether you think yourself right about a certain problem, have thought about it for a long time before coming to your own conclusion, doesn't preclude new, original information, or intelligent arguments to sway your opinion. I'm often pretty darn certain about my beliefs (those I care about anyway, that is, usually the instrumental beliefs and methods I need to attain my goals) but I know better than not to change my opinion or belief for a topic about which I care if I'm conclusively shown to be wrong (but that should go without saying in a rationalist community).