When I go to my homepage I get "404 Not found" article

When I go to my homepage www.site.com I get "404 Not found" article, going to www.site.com/index.php works fine.

This is probably because you have set the index file of Apache to something other than "index.php". You can remedy this by adding a line to ".htaccess" (or correct it in the virtual host configuration):

DirectoryIndex index.php index.html