GNOME 3 uses an entirely new interaction model which I, as said, have not yet experienced. This makes it difficult to properly cover this subject, and as such, I think it makes sense to focus on the reasons given, as well as list a few of my own concerns that haven't been addressed.
Let's focus on minimising first. The biggest reason behind removing this button is a very practical one: GNOME 3 has no place to minimise windows to. There's no taskbar or dock, and I guess my personal favourite (iconification) hasn't even been considered (that makes me a sad unicorn). Without such a place to minimise to, it indeed seems to be incredibly counter-intuitive to have windows minimise to... Nothing? Users would be flummoxed by disappearing windows.
The second important reason to remove the minimise button is that the GNOME 3 developers believe that workspaces and activities are sufficient and can replace the need for minimising windows. "Want to see a particular window? Go to the overview. Want things to be neat and tidy? Organise them using workspaces," explains GNOME's Allan Day, "A lot of work has gone into designing and implementing both the overview and the new workspaces functionality - we want to focus on the best parts of GNOME 3 rather than carrying incomplete legacy functionality. And focusing on one set of functionality results in a more streamlined user experience."
As for the maximise button, the reasons behind that change are pretty similar to reason number two above: there's new functionality in GNOME 3 that will replace the maximise button. GNOME 3 basically implements Windows 7's Aero Snap (I love it when good ideas are copied - and thus why I hate the current patent system), and the developers believe the dragging/snapping functionality of the titlebar in GNOME 3 can replace the maximise button. Double-click-to-maximise still works (and I hope the feature of double-click-to-minimise which I got into GNOME through a bug report does so too). Keyboard shortcuts are still in, too.
All in all, these reasons seem somewhat sound, although there's a couple of things they're leaving out. First, there's the discoverability issue: the Aero Snap-esque titlebar operations are essentially gestures, and gestures are notoriously undiscoverable. New users will have a hard time finding out they'll need to perform gestures with the titlebar to maximise their windows.
Second, and more importantly in my book, click and drag operations are incredibly intensive. With this I mean that dragging requires a lot of muscle tension, and is incredibly uncomfortable. I think user interfaces should strive to reduce the number of drag operations - not increase them. This is my biggest worry.
However, as said, I haven't the time right now to actually use GNOME 3, so I'll have to reserve judgment until I do. You guys, on the other hand - don't.