Thinking about it some more, it really is about consistency regarding the cursor. On my trackpad, not in "natural scrolling" mode, I get this:

  - One finger down moves the cursor down through the text.
  - Two fingers down moves the cursor down through the text (moving the text up)
  - Thumb-click plus one finger down moves the cursor down through the text (and selects).

in Natural Scrolling you get:

  - One finger down moves the cursor down through the text.
  - Two fingers down moves the cursor up through the text (moving the text down)
  - Thumb-click plus one finger down moves the cursor down through the text and selects.

If you start scrolling with two fingers and release one, the cursor reverses direction! This inconsistency just really feels wrong to me, but I guess you can get used to anything.