We did a lot of travelling with the kids when they were young but 3 is very young. I think our first trip was to Borneo when my youngest was 4 and that included only four nights of wildlife and jungle.
Just remember the distances in the US are vast. Places that look close together on a map can take hours of driving and the little ones could get very bored very quickly.
If you want to do a road trip I would recommend doing San Francisco to San Diego down the Big Sur (coastal road - think Cornwall on steroids!) and via LA. It’s a beautiful road and there are fun things for kids to see en route - Alcatraz, the Monterey Aquarium, lots of sea lions and elephant seals, Disneyworld, Hollywood and the San Diego zoo. Hearst Castle is amazing too. You’ll always have somewhere nice to break up the journey. We did it before kids in a week but doing it in two weeks will allow a much more leisurely approach. If you want to do it with hotels there are some beautiful ones to stop at. You could also do Yosemite and the Redwood national parks at the start although I’ve not been to those so not sure how suitable they’d be.