Yeah you literally can't leave a single thing visible in your car in SF. Car break-ins and bike thefts are the top two crimes in SF. Even in my hoity-toity neighborhood I see broken glass on the sidewalk sometimes.
As for things in SF you can't skip if you have only 1-2 days:
1.) Driving across Golden Gate Bridge up to the Marin Headlands. It's beautiful up there and you have an amazing view of the city and GGB. While up there I would also strongly consider Muir Woods - especially if you've never seen redwoods. It feels like you're walking through Jurassic Park
2.) Alcatraz. You need to book early due to popularity. But it's totally worth it. Definitely one of the best tourist attractions in SF. The boat also departs from the Pier 39 area so you can check out the Fisherman's Wharf touristy shit. I personally hate that area, but it's a big tourist attraction. But I do enjoy the sea lions and the really weird
coin-operated museum. Some creepy ass games back then.
3.) Given your short time span, I'd probably choose one neighborhood to explore in the actual city. Normally I'd suggest the Mission but it's not quite as kid-friendly (except for maybe
Dolores Park) since it's more hipster. North Beach (Little Italy) or The Haight (where Grateful Dead started off and hippies lived) might be better. What are your kids into? Might be able to suggest something better.