I don't know for certain if MTV have any special deals with the music companies (I did used to work for EMI but not in royalties) but everyone who plays music public needs to pay for it. This includes radio and TV stations.

I think the point probably is that music videos tended to be given away as freebies (although public playing of them would still incur a royalty payment) but now the music video is seen as part of the sellable product. I was actually part of the team that helped implement the technology part of this at EMI some years ago.