When the first X-men film was made (and with it, some would argue, the birth of the modern age SuperGenre) there was very little to establish a conflict of interest: in fact quite the opposite.
Lee was probably very happy that Marvel Characters were being transferred to the big screen.
As time has passed, and Movie Studios began to realize how lucrative these films can be (particularly post Spider-Man), the legitimization of the Marvel 'brand' has since housed itself within Marvel Studios (who are responsible for the MCU), as this is considered the transmedia syndication of the original Marvel Comics movie arm.
As such and without tacit acknowledgement, Lee mainly seems to make cameo appearances within these movies, as they are the ones that are directly contributory to his property empire. The exception to this rule is Spider-Man, which is understandable given his investment in the character and its contribution to his personal legacy, and there are other exceptions as well.
Basically, Lee only makes cameo appearances when his endorsement is considered financially lucrative or it simply suits him to: he is under no obligation to make a cameo in every Marvel Movie.
See also: Blade, The Punisher, the forthcoming Guardians of the Galaxy, etc.