Right now it typically is busy in the Santos area, but if you are looking for more peace and quiet you can head down toward the Land Bridge or even park down there. After you leave the Santos and Vortex sections, it typically is a lot less crowded even on busy weekends.
If you really want to get away from crowds on a busy weekend, the hard core local riders know to head to the far end of the trails. I'll just say there is some super sweet singletrack at the far southwest end of the Santos trail system and you won't find many people out there. Park at the Land Bridge or even 49th Avenue.