I ride in Yosemite every year--I've gone down there with the same group of friends every October since the early '80s, before we had kids, and now the oldest kids are pushing 30. we've done Tioga Pass in both directions (I was young and strong once) and all the main roads into the park, plus every paved road in the valley.
Main reason you don't see more bikes around the area, I think, is that many of the roads have no shoulder and at least in summer, the car traffic is heavy, impatient and rude. Plus it can be really hot on the west side, from the Central Valley up into the park, but it's the lack of shoulders that stops me.
If you get a chance to go back, try it in the fall. The crowds drop by two-thirds after Labor day, and the weather's usually good until late October or early November. I live in Reno, and the last weekend in Oct. is a Nevada state holiday. Most things are still open, but there are no people to speak of.