/index.php? to /

Yeah, OK... That's fun. But what about url generated by ez ?
I put the .htaccess on my website and it works. If I write www.example.com/fr I go on www.example.com/index.php?/fr .
But now I just can't browse on my site because all urls are still written with index.php?.
So if I click on the home link, I go on www.example.com/index.php?/fr and it abviously doesn't work.