I try to sync one location with another including subfolders except for folders that contain "svn". But regardless of what I put in the Filter Box, dopus syncs these folders too.
The synchronize tool is file-based so you may need to exclude files based on their location (i.e., no match *.svn) instead of excluding folders.
A subfolder clause that doesn't match .svn probably should work but I'm not certain off the top of my head. Could you post a screenshot of the filter you were trying? If it looks right but doesn't work I'll file a bug report/feature request (or you can file one yourself via the GPSoft support page).