Pathogen will not manage (update, install, etc.) your plugins for you. You have to do that yourself.
And a good way to do that yourself is to install plugins simply by cloning their Git repos to the ~/.vim/bundle folder. Then you can update them with one-line loops. For example in Bash you could do this:
for i in ~/.vim/bundle/*; do git -C $i pull; done
And on Windows you could do this (assuming Git is in PATH):
for /d %i in (%userprofile%\.vim\bundle\*) do ( git -C "%i" pull )
If your plugins have submodules, you can also add
git -C "$i" submodule update --init --recursive after the pull (on Windows change