Yet another way to do it is to specify an exclude pattern, so that rsync won't touch the .htaccess file.
rsync --exclude-from=/home/user/.rsync/exclude.pat ...
And the exclude.pat file should be in this format:
- /.htaccess - .htaccess
The first entry will tell rsync to exclude only the root .htaccess, the second one - to exclude all .htaccess files within the synchronisation tree. You can look it up in the rsync manual.