If you're taking an interstate flight, you are definitely engaging in interstate commerce. Even for intrastate flights, you are using the interstate air traffic control system, and therefore subject to federal regulation under the same clause.
Requiring a Federal ID to open a bank account or take a job is necessary to enforce Federal immigration law, under which one must be a citizen or legal alien to engage in such transactions. Therefore Congress has the power to require Federal IDs for such transactions under the elastic clause. The same clause gives Congress the power to enact the current Federal law that requires some government ID to open an account, though it is the enforcement of Federal tax law that is the aim in this case.
Again I ask you, what freedom are you giving up by having to show a passport to get a job?
"Gosh, Mr. Smith, we kind of lost your passport paperwork. Our shop steward was a wee bit miffed at some of the stuff you wrote about Hillary Clinton in your local paper, and that kind of hindered our due diligence. It's going to take us a few years to straighten this out. Sorry for the inconvenience. If you cheer the shop steward up a bit, maybe that will speed up the process."
If your ability to earn your livelihood depends on having a federally-issued piece of paper, you are now the servant of the people who process the paperwork.
Being the servant of a government employee is, the last time I checked, not any sort of freedom.
Nonsense. Federal immigration laws have been enforced for decades without doing any such thing.
All it takes is spot-checking known suspicious employers often enough, and setting the fines high enough, so that the "expected value" (the amount of the fine multiplied by the probability of getting caught) of the penalities exceeds the savings from hiring illegal aliens instead of citizens. That's Statistics 101.