Here's my general view of it. We know Jonathan oversees day-to-day operations. Bob might set organizational strategy, but he's not managing anything directly. That's Jonathan. The Krafts have a number of different holdings, so there's likely a point person for them at each. Robyn Glaser appeared to be that person for the Patriots.
From the stories I've heard about Jonathan with the boards he's involved in, he's very much a classic cost-cutting businessman. So Glaser was just following his directive. She still deserves some level of blame because Jonathan might say something like "cut costs by X%", but he's certainly not going to review the line item budget himself. That's Glaser's responsibility.
So in terms of Bob being cheap, I'd say it's more that he could have directed Jonathan to adjust the team's financial strategy, but chose not to. The family owns 100% of the team, so it's not like he's got minority owners who want him to maximize shareholder value. Any profits go into his pockets, so it's up to him to determine how he values those profits versus team performance.
Really, it's probably the fact that they had 20 years of success, despite keeping costs low, and given what we've learned about his ego (in terms of Bob believing he deserves as much credit as Brady and Belichick), he probably thought he ran a perfectly designed organization, where the reality is that they likely won in spite of him.