A few reasons:
1) The majority of Al's (non-animated) videos were filmed before Rubén joined the band (in the 80s, when music videos mattered).
2) Rubén is primarily a touring keyboardist. Therefore, if he's not available the day of the shoot, they would probably just go on without him as opposed to, say, Jim, for whom they might reschedule part of the video shoot.
3) Al and his record label would be able to save money by having to pay fewer band members to show up, especially a band member who does not play on the song. Other than The Saga Begins, can you even think of the last Weird Al single that Rubén plays on?
4) Rubén is just so freakin' ugly, Al didn't want to feature him prominently. This explains the Darth Sidious hood in The Saga Begins.
born this woway