You can ignore .git folders before initializing your repository [0]
[0] http://aditya.vaidya.info/blog/2013/08/25/using-dropbox-and-...
[0] http://aditya.vaidya.info/blog/2013/08/25/using-dropbox-and-...
I believe a perfect solution for power-users would be a support for '.nodropbox' files, which would disable selective sync for a given directory and it's subfolders.
An even better idea would be '.dropboxignore' files, using the same syntax as '.gitignore'.