There’s no “right” way. It’s all in the analogy.
The Touch Screen Analogy
When you use a touch screen, the scrolling behavior is intuitive — it’s like you put your finger on the actual content and push it around. A few years ago, Apple switched their scrolling direction to follow this analogy.
The Scroll Bar Analogy
Another way to look at (Windows-style) scrolling is that you are interacting with the scrollbar, rather than with the controls. Apple is not keen on the whole concept of scrollbars currently, and hides them in many contexts by default. This pushes the concept of scrolling gestures interacting directly the content.
The Mouse-Wheel Analogy
The first trackpad scrolling mimiced how mouse scrolling worked. And the first scrolling mouse had physical wheels (many still do). If you imagine the scroll wheel sitting on a paper you were reading, the “Windows” scrolling direction is intuitive — the content moves in the direction the wheel would push it.
Apple mice don’t have these physical wheels anymore, so they are pushing for the touchscreen analogy for all their scrolling devices. But when I plug my old-school mouse with the real wheel into my Mac, the Apple’s “Natural Scrolling” doesn’t feel so natural anymore.
Your Brain doesn’t really care
Users generally find it takes just a moment to adjust to the new paradigm when the scrolling is working the opposite way. I don’t know of any “regular Joe” users who get upset about this, they jiggle the scroll a moment to get used to it, and start using the device.