You could create symbolic links from .htaccess to htaccess in each directory so you will have a reference to the hidden file you can access from within Finder(or other applications).
To do this just go into the directory in question in Terminal (
cd /Path/to/directory) and link the files (
ln -s .htaccess htaccess). The -s makes it a symbolic link, which means it references the original linked file instead of creating a second file. When you edit htaccess you will actually be editing .htaccess
Hope this helps, you can read
man ln for more information on linking files.
Another solution would be a software add-on to Finder that allows you to filter files out from the listing. I don't know of any that do this, but it is what you would want to look for.