.gvfs directories are mount points (sometimes). You may want to use the
one_fs option in your rsnapshot configuration (so that it passes
--one-file-system to rsync).
Gvfs is a library-level filesystem implementation, implemented in libraries written by the Gnome project (in particular
libgvfscommon). Applications linked with this library can use a filesystem API to access ftp, sftp, webdav, samba, etc.
Gvfs is like FUSE in that it allows filesystems to be implemented in userland code. FUSE requires the one-time cooperation of the kernel (so it's only available on supported versions of supported OSes), but then can be used by any application since it plugs into the normal filesystem API. Gvfs can only be used through Gnome libraries, but doesn't need any special collaboration from the kernel so works on more operating systems.
A quick experiment on Ubuntu 10.04 shows that while an application is accessing a Gvfs filesystem,
~/.gvfs is a mount point for a
gvfs-fuse-daemon filesystem. This filesystem allows any application to access Gvfs filesystems, without needing to link to Gnome libraries. It is a FUSE filesystem whose implementation redirects the ordinary filesystem calls to Gvfs calls.
gvfs-fuse-daemon filesystem does not allow any access to the root user, only to the user running the application (it's up to each individual filesystem to manage the root user's permissions; a classic case where root doesn't have every power is NFS, where accesses from root are typically mapped to nobody).