which window manager are you using ? probably gnome or kde ? CTRL and ALT keys and ALT-MMB are already binded in those window managers so you have to CHANGE this by hand. There are detailed instructions with your linux maya package on how to do this... its simply done through the window manager's configuration utility .... ( kcontrol for kde and ... i dont remember how it is called in gnome... ....)
I have experience on using maya with Linux though i currently work on windows



Konstantinos