The truth is there is no one answer for why this is the case, there's a bunch of factors:
Whilst PC gaming is on the rise, only a minority of PC-gamers are actually mod players, and the bulk of those who are mostly playing mods for games like Minecraft or Skyrim that are well supported and easily integrated. Whilst installing GE:S is easy, people who haven't played mods before aren't prepared to take the plunge, especially when they are used to services like Steam where everything they need to do to install something is very straightforward and simplified to the max. This is mostly a perception problem, whilst mods are awesome there is the common belief, that is historically quite well founded, that installing mods is fiddly, time-consuming, difficult and very often not worth the pay-off. Nobody really wants to go to this site, and download this, and make sure the version is up to date, and then install this other thing in Steam and blaa blaa...
On top of that, most people already have multiplayer games that are their go-to games for online play and GE:S isn't something that, for most people, can fill that niché. Even indie games with multiplayer struggle to have even the remotest active community. A lack of players is a vicious cycle of death for a multiplayer game. No players > No servers > No players > No servers... This is something that has burned a lot of smaller indie games that attempt multiplayer. An absolute killer of GE:S is that many new players often come in, see nobody playing online in the server browser, so they quit and don't try again. I can't count how many times I've read comments on videos with things like "Nobody plays the mod" or "The mod is dead."
The biggest overall reason is just that we're not on Steam. Mods like Fistful of Frags and Neotokyo are, and they have healthy communities mainly due to it. Without being on Steam we can't roll out regular updates automatically to installed users and we can't quickly patch out minor issues.
Another reason is that moddb's download server is just absolute awful. I recently introduced some new players to the mod and they were complaining at how long the download from moddb takes. Plus many people end up with corrupted downloads as we saw with 4.1's release. We need more download options, that's something we can definitely improve on.