Because you're used to have the choice of installing 'for me' or 'for all users' for aeons now on a Windows system.
Because even my tiny deployments are better and safer if I can make sure that FF is updated for every user of my machines, instead of hoping that they'll get an update next time they browse Facebook.
Because it's wasteful to install the very same software to different places. Yes, storage is cheap on modern hardware. No, not everyone uses FF on modern hardware.
Profiles belong to the user. The application belongs - in a Windows world, in a Linux world - to the system / administrator.
Love the mozilla guys for keeping the expectations intact. Re: "Program Files": Maybe ProgramData would be a decent place to drop updates. Program Files is supposed to be readonly, ProgramData is afaik the place designated for system-wide application data.