It has been my experience that running Linux natively on Apple hardware is a huge pain.

My experience runs 100% opposite to yours: I got a new Macbook Pro, installed Ubuntu on it, and have been running it just fine alongside OSX for months now, with no issues. In fact its running so well that I no longer need my Linux workstation PC, which I .. might .. just turn into a Steambox..

Anecdote: I've been running Debian Stable on a Macbook Air I bought in 2011 since then, it's been great (and doubly great since Wheezy, the support is basically 100%).

Not anymore. It's flawless for myself (iMac from late 2011, MacBook Air from 2009).

but why? if you paid for Apple hardware, OS X is ten times nicer than ubuntu.

Ubuntu's not the only choice, though.

Apple has a hard time matching the speed and flexibility of a lightweight GNU/Linux distro (presumably because OS X's focus on polish, integration and aesthetics means they want to tip the scale of compromises back in that direction, and that's fine). Some of us don't mind not having drop shadows and pervasive "cloud" integration if it means we can have full control over our own computers :)

That's a matter of opinion.

OS X has better support for its own hardware, like the trackpad. How can that be a matter of opinion?

That OS X has support for it's own hardware is fact. That OS X is better than Ubuntu is opinion.

It's also worth mentioning that Ubuntu has perfect support for the current Macbook Pro and Macbook Air, so I don't know what point you're even making by saying that OS X has hardware support for Macs.