Your subscription fee goes to Square-Enix.

The Mogstation profits specifically go directly to the team working on FFXIV.

That's why I support the Mogstation. Yoshi's even flatly admitted it was because of the Mogstation they could do stuff like get new datacenters, which have been a lot better than the old ones by a noticeable amount. The Mogstation funds things that the parent company, SE, won't necessarily fund. There's even a fairly reasonable chance that the Mogstation helped fund Viera and Hrothgar, to be honest--as those were both things fans were wanting and got (admittedly not in the way people probably wanted them, but still better than none at all, yeah?)

This really really does boil down to: If you don't like it, that's fine, don't buy stuff from the Mogstation. But the Mogstation is overall much more beneficial to the game than not having it, despite how gloom and doomy people get about not getting some outfit or mount they wanted.