I found that I can use:
ignore.default = \A#.*\Z \A.*~\Z \A.*\.py[oc]\Z \A.*\.sw[nopx]\Z \A.*\.swpx\Z \A\..*\.tmp\Z \A.*\.git\Z
In /etc/xdg/ubuntuone/syncdaemon.conf to ignore files. I'm not really up on regex so I tried to add the last line to ignore the .git folder. It doesn't appear to be working though. Anyone have a correct solution?