Wordpress creates the .htaccess file with 600 file permissions (when permalinks are configured, etc.). I had to give it 655 before SuPHP would allow the homepage to load. I thought any files should be read as the user with SuPHP so I'm a bit puzzled here. I'm trying to replicate a shared hosting environment so non-developers and setup CMS'es without difficulty so this is a showstopper for me. Thanks for any help!
You need to chmod .htaccess to 755 in order for it to work, otherwise you will still experience this issue. If you need to do that automatically for files created by apache, please check the next link: