http://www.popeater.com/2010/04/09/bones-moonlighting-effect/

The show's ratings decline is popularly attributed to Episode #14 of Season 3, "I Am Curious... Maddie", which infamously had Maddie and David consummate their relationship after two and a half years of romantic tension.

Whether that was the real reason the show's ratings declined, it is evident that many tv producers are fearful of getting tv love interests together mid show.

One can argue that what tanked the show/made it jump the shark (https://web.archive.org/web/20061031125239/http://www.jumptheshark.com/m/moonlighting.htm) really wasn't David and Maddie sleeping together, but the contrived ways the show tortured their relationship to cover both Bruce Willis and Cybill Shepherd not being full time available. Had the show continued normally with David and Maddie still constantly fighting but in the context of an actual relationship, then maybe the show could have still worked well. But Willis needed time off to make movies and a recover from a skiing accident and Shepherd needed time off after she had twins. The show could not figure out how to handle their absences--if there weren't ever in the same room, there couldn't be any of the tension that made the first 2-3 seasons so fun.

And the long delays with no new shows ; repeats didn't help. Hooking up didn't hurt the show Bones and some others.