I hate having dotfiles in ~/ for the same reason why I hate "My Documents" in Windows: because it's supposed to be my space that I organize, not a generic dumping ground for your config files, brand-named folders, or other nonessential garbage. I want my space to be mine . Keep your app's stuff out of there!
"My Documents" is a nightmare... I think only one folder (out of nearly a dozen) and only one file are actually of my making.