Because it used to not be hidden and it was there and visible when ever people opened their home directories. And when people went in and decided to to "have a tidy up" bad things happened.

People stumble on /Library a fair bit less and Apple took the different approach of locking it down through permissions (users need to be able to write to ~/Library regularly, /Library not so much).

And I guess people clear about ~ because it has meant the user's home directory in Unixy shells since about the beginning of time