Bryan Singer still has a very strong relationship with Warner Bros., who is distributing his next film Jack the Giant Killer
. It was probably more of a case of Warner Bros. deciding to go in a different direction, similarly to how Tim Burton wanted to do another Batman movie after Batman Returns
but WB talked him out of it (at least, according to Burton).
The same thing probably happened with Singer- after all, he did talk to some degree about his plans and desire to do a Superman Returns
sequel, and obviously based on Michael Dougherty's comments, and based on this story treatment, there was enough development work on this to confirm that at some point or another Singer thought he was going to make another Superman movie.