Yeah I always figured it was because fonline is basically a modded version of fallout 2, which technically means it is still creating fallout 2 sales and that it isn't an independent game/dev group cashing in on the name by selling the game or their modded version, it is fans paying to provide servers for an online mod of the game, created by fans.
It would be really weird for bethesda to attack these projects as they are, it would be like if Rockstar sued someone for hosting a server of a modded version of GTA, it just wouldn't happen. The little gain on their behalf far outweighs the effort of shutting it down for no gain (or a loss).