Money is almost certainly a factor, perhaps the driving one in the case of Brookline. Money to compensate TCC for the kinds of repairs and inconveniences outlined by Brad, but also in terms of how much the USGA will "get" from hosting the US Open, and what % the club might want to keep for putting up with hosting the carnival that is the championship.
It's also reflective of the changing dynamic of how the USGA selects the US Open course. It's clear they are moving toward a more "public" model of utilizing courses, i.e., Bethpage Black, Torrey Pines, Erin Hills, Pinehurst 2, Chambers Bay. There is certainly less hassle with the negotiations over money, and increasingly the publics view hosting the Open as a plus for future revenue and prestige. The well-established privates -- notably Winged Foot, TCC, Shinnecock Hills -- don't necessarily view hosting the Open as a plus, already have the prestige, and don't need the publicity to drive revenue, because they often have well-established, long-standing members.