FWIW, my question doesn't only pertain to D1. There are also D2 and D3 programs out there that consistently lose twice as much as they win and the question pertains to them as well. I meant college baseball as a whole.
And, I agree that the school and education come first. You should pick a school based on that and not the strength of the baseball program. That said, no matter what the school, no one is forcing you to play baseball and that's always a decision to be made.