> Let's take the movies "The golden compass" (The golden compass) or "John Carter" (A Princess of Mars) for exemple. Would that be possible for a director that loved one of these books to make a new movie about it ?

Sure, go buy the rights.

> Or will it be harder for him to obtain funding from productors since the disney movie already failed ?

Yep

> It happened for other movies like "The lord of the ring", but could it works for a book that is less known ?

It has happened many times.