I've been there riding twice in the last couple years and had pretty good experiences-- mostly. See below.
There's a pretty casual loop around Mission Bay, mostly on bike paths; you can park/start at Dog Beach in Ocean Beach or at the convention center right near Sea World, then ride on the paths that follow the shore. The bike layer of Google maps shows them clearly.
If you park/start at Liberty Station, riding from Point Loma along the bay to downtown, between Harbor Drive and the water, is fun and pretty. You can end up where the ferry goes over to Coronado Island, then ride to the beach. This would be an out-and-back.
Last, and most interesting but also probably most challenging, would be riding the point out to Cabrillo National Monument. Extravagant views, tide pools, the occasional hard climb.
Your caution about bike theft is legit. My bike was stolen there in August, downtown. Bike shop folks and a facebook group maintained for victims of bike theft all suggest that the problem is systemic, widespread, and severe. If you want to ride downtown, or really anywhere that you'd leave your bikes unattended for any period of time, look online for the (relatively few) places that offer an indoor, secured bike lot; the transit station near the ballpark is one, but there are probably others. If I had it to do over again, I would rent a Jump or other short-term bike for any ride that would require locking it to a rack out of my line of sight in San Diego. I don't know how the problem compares to other cities.
Good luck, and have fun. It's a great place to ride.
John