Check out Savage 2:

http://www.savage2.com/en/main.php

From their FAQ:

"What is Savage? What type of game is it?

Savage is an RTS/FPS/RPG hybrid. The setting is a post-apocalyptic world where the Legion of Man and the Beast Horde battle for supremacy. There are two teams in a game of Savage2, both of which will expand to capture resources, kill enemy players and NPCs, and build up their bases to unlock new technology or magic to try to crush the enemy base. Victory is achieved in Savage 2 when you destroy the enemy command center.

Part of what makes Savage 2 unique is the role of "commander" - a unit who plays from the RTS perspective and helps organize his team's efforts to defeat the enemy. Commanders can build structures, buff allies, debuff enemies and most importantly play as master tactician with a great view of the battlefield. A lot has been done to ensure that the commander is not overpowered or able to ruin a game for his team."

It is completely free to play and has a native Linux client. The community is rather small at the moment, because it has a bit of a learning curve, but once you mastered it (and that shouldn't be a problem for any Linux user), it is one of the best multiplayer games.

Note that the other games S2 games has developed also have native Linux clients.
Check out Savage 2 for example which is a great game and available for Linux
for free:

http://www.savage2.com/en/