First of all, you should not get in the habit of editing *nix "text files" (like .htaccess) in WebFtp.
From the Dreamhost Wiki Article on CGI, PHP, and Databases:
Your best bet is to use a shell text editor, such as pico or nano, to work on such files (which will also eliminate any "permissions" strangeness you see using WebFtp as an editor when trying to save the file).
Alternately, of course, you can use a pure "text" editor on your own computer, and just upload the resultant file(s) via ftp to the appropriate place in your directory structure. Look for an editor you like that is capable of saving "with nix line endings", or run "dos2unix" from the shell to "post-process" such files. Finding an editor that uses *nix lline endings it the better way to go. There are *lots of them out there that are free - just google and try a few till you find one you really like.