The issues are two fold. First and foremost Minecraft has always been a Java game, that's how this whole thing started. Therefor it has always been called "Minecraft". If you mentioned "Minecraft" you were referring to the Java edition.
Not only has Mojang renamed 'Minecraft' into 'Minecraft Java Edition' they also renamed the Pocket Edition (or mobile or whatever) into 'Minecraft'. So now if you mention 'Minecraft' they're trying to make it so that you're actually talking about the pocket/mobile/etc. edition. And that ticks plenty of people off because Minecraft has always been Java. Basically, according to some players, the original players of the game have now been moved to the sidelines and they're no longer considered official Minecraft players. Instead anyone playing the mobile editions are now considered "official" (note: not my opinion but just what I perceived around me).
The other issue has already been mentioned by others: the fear that Mojang could very well focus their attention completely onto the other platforms and discontinue support for the Java edition. I think those are valid concerns because it is a fact that Mojang / Microsoft might be able to make a whole lot more money on those "portable platforms". Where we can simply download any skin we'd like you'd have to pay for it on the console editions.