I use drush make with a stub .make file to download a custom profile via git.
that profile has all of the modules I want all of my sites to start out with.
If I then go into that site, and run "drush up drupal", it will update core, and remove my custom profile.
This is not good, since all of the modules I downloaded with my install profile's make file get stuck into the profiles/myprofile/modules folder. This basically removes all of my installed contrib modules, and drush doesn't give me a way to put them any where else, so basically, I can't update core with drush.