First off yes, we know how some people view this word and the stigma attached to it. "Otaku" has the same irreverence attached to it that the term "nerd" did no more than 30 years ago in the U.S.
However Otaku isn't a term used in good humor in Japan, so why use it? Well, that's simple; it's used as a term representing someone who is knowledgeable or a fan of something specific. There is no difference in being a computer otaku or a computer nerd and, in all respects, it is the same term.
So in light, we don't see it as a term of disrespect but a term of endearment!
As the convention and anime culture has grown in the U.S., so has the way we have expressed ourselves. We are no longer a stay-at-home group and more Otaku, or fans, have eagerly assembled with those like them. We respect what the word means in Japan, however we still choose to use it as part of our name.