I know that in the US and in India people flying on domestic routes are required by the government to carry photo ID. I could understand why the airline might want to check IDs - it's helping them avoid scalpers and ticket resellers. But what's the point of that requirement from the government's point of view?
In theory, everyone who gets through security are supposed to be checked throughly, so it should be completely irrelevant who's actually flying the route. Likewise immigration is not a concern on domestic flights so again the identity of the traveler should not be of concern.