It's the hardware, stupid. :-)
I mean, compare: http://www.apple.com/macbook-air/
with: https://www.crowdsupply.com/kosagi/novena-open-laptop
(ok, you could also buy an Asus laptop or something that would be nice looking enough, and cheaper than a novena laptop).
Another point, is that when you're at home, with a linux laptop, you can spend two days configuring the wifi. But when you're going out to a conference, MacOSX shows its worth.
Oh, and for several MacOSX versions now you can map the modifier keys as you wish, in the System Preferences / Keyboard panel.
MacOSX is not entirely proprietary. Darwin is open sourced (in large part). And as developers, we use a lot of free software on MacOSX, starting with emacs, and all the linux tools you can get from MacPorts or Homebrew. Right, because between ourselves, the BSD tools provided by Apple suck.
But actually, it's the econony, stupid! ;-)
As a Linux hacker, I much prefer to earn the money I need to pay for taxes, internet, electricity, food and shelter (oh, and clothing, sometimes you get to go to conferences), developing applications on a unix machine like MacOSX, or iOS, rather than on MS-Windows. (Yes, there's also Android, but java...)
So don't make a mistake, the main workstation is a Linux box, and even while developing MacOSX application, most of the code is written from the Linux box, even if it's compiled by Xcode on the MacOSX system nearby. Because, honestly, Linux is much more ergonomical! (if only because you really can configure it as you wish (and also strangeley, the keyboard feels much more responsive with linux than with MacOXS, let alone MS-Windows)). Anyways, remember, the Network is the computer! But most customers are still MS-Windows users, or MacOSX or iOS users, (or Android users right). So while you keep Linux close to the heart, you have to have a MacOSX system to earn your living.
(And there's also the possibility to run MacOSX on a Virtual Machine on Linux, but let's be honest, it means that legally you still have to own Apple hardware).