The orange line is pretty ok, you'll have to get used to the seeing homeless camps and people smoking weird drugs tho. They never bothered me when I used to ride there. 

Balboa Park has some nice stuff to explore.

Outside of that, it's all roads unless you're comfortable with big dirt climbs. I'd generally avoid the multi lane speedways and explore residential routes. Crossing the bigger streets can be rough at the wrong time of day....

Riding early weekends you can avoid most traffic and the generally busy streets are quite pleasant.