Alternate theory: The Internet is a dangerous idea – cf Raganwald last post. Religions would probably prefer to keep followers away from the web and in a place of worship, where there is more direct idea control; therefore would be less interested in devoting resources to developing websites. Second, I’d suggest that the average hacker puts reason before faith, so is less likely to believe in a supernatural creator.
I don't agree at all with your first point. The internet is just a communication tool, albeit far more powerful than ones that have come before it. This means that it can be used to build religious organizations or proselytize just as easily as it could spread knowledge about secular humanism or whatever.