Yeah, Hindsight is 20/20. At the time it was a great idea. Had they known they would one day start their own successful independent film company and then later be bought out by Disney and gaining a bottomless wallet with which to make any film they wanted, they wouldn't have made those deals. But they didn't. Hell, if they didn't sell those film rights, X-Men wouldn't have been made and started the huge comic film boom that made their little independent film company happen, which lead to Disney deciding to buy them out in the first place.
Still, when you consider all the money they have made and will make off the movies all these other companies are making, they've got it pretty good. If it sucks, eh, they still get paid.