This is a common misconception. MS-DOS is/was a 16bit command-line environment. It is no more "under the hood" than Notepad. The cmd.exe program is merely a console application designed to roughly emulate the old MS-DOS program command.com with some extensions and changes.
This criticism was often leveled at Windows 9x too, but it was still wrong (for essentially the same arguments above). However, in the case of Windows 9x, MS-DOS was used as a significant part of the boot process.
The Windows 2000 logo states that is was built on Windows NT. I wonder if Windows 7 will be built on Vista or XP. It would be a wise decision to go back to XP as the base and merely lift Aero from Vista. (UAC needs to be redesigned from scratch - they got it all wrong.)