A very large percentage are early beta releases with many features planned either not implemented or still in the testing phase, and so pulling people away from a mod which is polished, plays well online, and is fun to play is very hard indeed. With CS taking the limelight, it's true that other mods have been thrown by the wayside because maybe the media and community felt they didn't measure up to CS, or simply that their public releases were over shadowed by maybe the latest Gooseman interview or CS Beta screen shots. I know it has happened, even recently. Different, I think. It's not logical to assume that everyone that plays Counter-Strike today, would be in the community now playing something different.
Different mods attract different players.
As 1999 continued, and the CS team released beta after beta, CS was gaining in popularity and was catching the eyes of many - including Valve. With the tools for mod making being fairly user friendly, and with the Internet allowing communication with anyone in the world who has a connection, finding and assembling teams has never been easier. People have the ability to create whatever they want if given access to the tools and talent to make their dreams and ideas a reality. A lot of mods, however, seem to emulate CS in one way or another whether they mean to or not. Of course, it doesn't help, as I mentioned above, that the media will always compare your realism-based teamplay mod to CS whether you like it or not.