If you're using Eclipse PDT, this is done by opening up the PHP explorer view, then clicking the upside-down triangle in the top-right of that window. A context window appears, and the filters option is available there. Clicking the Filters menu option opens a new window, where .* files can be unchecked, thus allowing the editing of .htaccess files.
I searched forever for this, so I'm sorta answering my own question here. I'm sure someone else will have the same problem too, so I hope this helps someone else as well.