If someone constructs a railroad which operates entirely within a state and does not connect to the national railroad network, why should Congress have any authority over it?
If a trucking company operates entirely within a state, in a manner which does not interfere with traffic on public rights of way, again I don't see Congress' authority.
As a practical matter, I would think it useful for Congress to have authority over airspace and airwaves even for intra-state flights and transmissions, but I see nothing in the Constitution that gives it such authority. I also see nothing that provides Congress the authority to authorize long-term (over two years) appropriations for the Air Force (while it's possible that even the largest projects are produced without longer-term contracts, I wouldn't expect that to be the case).
Of course, the remedy for such shortcomings can be found in the amendment process.
Specifically? You're right. It's not there.
(Hoo boy.)