Chrissy Field is the best place to run in SF. The path is long and flat, and on sandy dirt (so your knees won't hurt from pounding the pavement). The views of the beach, the bay, and the Golden Gate Bridge are beyond comparison. Also, there are always SO many other people jogging, power-walking, biking with their kids - it really gets me more pumped about working out to know that there are people staying fit all around me. I park at the Yacht Club, where there are always available spaces, and then just start running towards Fort Point. I would definitely recommend this path!
Cons: not a lot of places to get food after, but you can always go up to Chestnut St