It makes perfect logical sense to me. It's not up and down, it's forward and back. Push forward and the nose drops, pull back and the nose rises. 110 years of aerospace engineering seems like a pretty solid place to start, and that's what these control systems are derived from. To me, most first-person video games are setup backwards, so I have to "invert" the pitch axis to normal. That may be where this idea came from, but I don't think it should be the standard.
Derived from? Sure, but not equal to. Look, arguing over which way it "should be" is pointless. The reason why I figured out the switch is so people would have an easy way to decide how they want to do it. Why advocate for taking away someone's choice? I like it this way, you like it that way. Big deal. Flip the switch and we can both be happy. I don't criticize others for having a different preference than I do.
Simply change the +/- of the tilt channel in the GUI. Want the tilt/pan on the left and the speed on the right, remap the channels in the GUI. Want a flying cap like Steve Maller's avatar (ok that one you can't do in the GUI). Just like Burger King you can have it your way