They make sense given the history of the Internet, but not in hindsight. Most obviously, .gov, .edu and .mil should be under the .us TLD, but obviously the inventor's prerogative applies.

It's arguably defensible to have a limited number of non-geographic TLDs. "Dot com" was an aesthetic as much as a technical decision. I wonder though, if .com/net/org had never existed, we would have a different sense of aesthetic around domain names, and there's no reason to think that it would be any better or worse than what we have now.