Both were instances of groups of queer people rebelling against the authorities after months (or longer) of mistreatment, harassment, and arrest. Why is Stonewall seen as a pivotal point in LGBTQ history and activism, while the latter not to the same extent? Was it the difference of those few years that allowed enough change for people to feel more emboldened/feel more hope after the former?
While I didn't use the Compton Cafeteria Riots as one my examples (I picked the New Year's Ball which came a bit earlier), you may be interested in my answer here, where I explain why the Stonewall Riots out of all the different incidents became the famous one.
The short answer on Compton's: it wasn't viewed as newsworthy at the time -- it didn't hit mainstream press like Stonewall -- and there was no commemoration event. Also, San Francisco homophile community (as opposed to New York City) frowned more on actual rioting. (In fact, the SF community was the slowest to pick up on celebrating Christopher Street for this very reason.) This was partially because they were more conservative in general, but also because they had achieved an equilibrium of sorts with police after the New Year's Ball events that they didn't want to disturb.