This has bothered me for years. Everything just looks so chunky and inelegant. The difference really hits home if you compare Rhythmbox and iTunes (OS X version, not Windows) side by side. Rhythmbox just appears to be wasting so much space.
Arguing that it makes the interface cleaner might seem correct in theory, but in practice it really doesn't seem to hold true. Especially when you compare to OS X, which has an extremely clean interface without any over padding of elements.
In addition to the excessive padding, what bothers me, is that the typeface choices in Linux are so oversized and ugly.
And the way Linux renders Segoe UI is ghastly compared to the Windows rendering.
If you want a smaller font size, you're out of luck since the padding seems to be assuming that you're going to have those big 5/20 vision fonts, so your buttons have a tiny bit of text in the middle, and acres of space round them.
Arguing that it makes the interface cleaner might seem correct in theory, but in practice it really doesn't seem to hold true. Especially when you compare to OS X, which has an extremely clean interface without any over padding of elements.