The thing is though, as it turns out, Bob's right and she's wrong.
As he says at the start 'no matter how many times you save the world, it always manages to get back in jeopardy again', and he's right.
The family's being screwed up by Helen's insistence on their not being who they really are. Dash is getting into trouble at school because he can't be competitive and Violet is a paranoid wreck, because the need to hide has been so strongly ingrained in her by her mother.
Bob really loves Helen, and the mistake he makes is that this means he'll go along with what Helen says, even though it's really wrong for his family and makes him miserable.
However, Helen's also really trying to do the right thing, because she thinks that the system will protect her family.
Her mistake was not to leave them babysitting - or to negligently allow them to come along - it was to believe in the 'system' and not to actually protect them herself, or allow them to protect themselves. It's only when she starts to really take responsibility, use her talents and abilities to protect her family, and tells them to use their powers, that the family really comes together. When she says 'run as fast as you can' that's when she really gets it and actually becomes a good mum.
TL;DR - Bob was right all along, except in giving in. The system sucks. Don't let the man get you down. If you're awesome, be awesome. But, you know, be a little bit discreet and gracious about it.