Because the season ticket holders opt to use the third party instead of the Yankees directly, so now they're losing out on money there. Instead of getting tickets for face value from the Yankees Stub Hub will sell them for cheap and sometimes they don't even get sold, so while the tickets get sold, the fans wind up not showing up and thus, not spending money on concessions and food and gear and stuff inside.
For the Yankees, fans win if they wanna get in the building (seats down low still cost a pretty penny). The Knicks /Rangers it doesn't work at all because you still have to suck some dikk just to get in, and for the Nets, let's just say if Dwight Howard had gotten traded there, I coulda turned 15 cent tickets into a shrewd hustle.