SimCity 3000 actually had a native Linux port by the (now defunct) Loki Games, that can still be gotten on Amazon and some other resellers and can be run with the help of some compatibility dependencies, although it's been some time since I tried.

http://www.lokigames.com/products/sc3k/

http://ubuntuforums.org/showthread.php?t=1300658

The Cities in Motion series (same developer) runs on Linux too, but those are more transit modeling than city building (but if you build roads, buildings will follow).

wait... what?!

HOLY SH*^%

If only it didn't require steam :(.