I just got back from a trip to
Disneyland, I'm in the Peninsula Bay Area so I'm north of you. We always drive down HWY 5 so I'm very familiar with its rest areas and other places along the way and back. When I go with friends we return down 101.
101 seems very plain and empty when it comes to places to stop and rest areas, there seems to be practically no rest areas and the few that you run into area DO seem very isolated, small, and scary. There's places to stop but they all seem so spread out and far from one another, and tricky to get to.
I would say your best bet is HWY 5. The rest areas are nice and large, if you're there during the day you will see a lot of activity, families, touristy looking folk, safe areas for the kids to run around, restrooms are fairly clean, usually have toilet paper, running water and soap, grounds people always around. *YES* of course you want to keep an eye on your kids and not let them use the restroom alone. We've even stopped at night, there's less people but the people we've seen are still families or weary travelers, we've never had any issues or felt unsafe.
I have a friend who doesn't stop at rest areas that often, I don't know why but she has stereotyped them as being creepy and unsafe, feels safer stopping at gas stations. Gas stations in my opinion are creepy and unsafe! Just about every time we've seen creepy men inside, and the restrooms are a nightmare - very dirty, very isolated, often outside and around the corner - where no one can hear you scream

!
Via HWY 5 Casa de Fruta will be your first largest stop, and long the way you'll have rest areas and large shopping centers with several fast food places and gas stations which are visible from a distance so you should have time to find the exit without missing it.
I think the Valencia Magic Mountain area is the last best place to stop, after that is when you really start to hit traffic and enter the busy freeway.