The relationship between Hitler and Roehm had become strained especially after Hitler became Reichskanzler. Hitler felt that after gaining some power it was time to tone back the violence and rhetoric of revolution. He wished to make The Party look more official and respectful and concentrate on more legal ways of gaining more power.

Roehm though felt that it was time to step up the violence. He felt betrayed by Hitler as he felt that a socialist revolution had been promised for a long time. He'd been ordered by Hitler to stop but continued anyway. He'd join the party expecting that one day it'd bring in socialism but Hitler had spent years moving the party more and more to the right, which of course culminated in the Night of the Long Knives with Hitler purging the party of its more left wing members.

However, before it became useful to use Roehm's sexuality against him Hitler doesn't seem to have cared and in fact pretty much said that.

This is covered somewhat in "Hitler" by Ian Kershaw.