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Well, you're really comparing apples and oranges, regarding the San Diego Comic Con, which is slowly being taken over by Hollywood interests. Nothing bad there, but as the "Twilight" fans are
In geek fandom (I've got over 30 years in the trenches), there have long been overlapping sub-divisions - comics geeks, anime geeks, literature geeks, media geeks (of various flavors, from Trek to BSG to Buffy and beyond). I think the clash at SDCC isn't representative; I think its a clash between primarily older, male comics geeks VS anyone who has primarily a media focus, who don't care about comics, and who they see as the harbingers of the media takeover.
Non-comic Geek culture, in general, is much more gender-balanced, and don't really bat an eye at Harry Potter and Twilight fans (both of which are dominated by very young, female fans).