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The Finder treats certain folders as packages of files that the normal user wouldn't want to see. Examples of these packages are applications and, well, packages :) If you select one in the Finder and hold down the control key while clicking (once) on it, you'll get a popup menu which includes "Show Package Contents" as an option. If selected, you'll get another Finder window that lets you look at all the goodies hidden away in there. Icons, scripts, different languages, sometimes even a bit of executable code :)

MobileMe doesn't do this when viewed through the web interface, because you might be looking from something other than a Mac, and then it's just a folder of random stuff.

All that said, I don't know why you should have gotten the error about running out of space, unless perhaps it wasn't the MobileMe disk that ran out of space but your own, and the error message didn't make that clear...