Aren't those state funds and not federal funds? It's a false equivalence regardless since college newspapers have a single campus audience while NPR is mainstream press. I don't believe the authors at college newspapers are typically paid either
Its an example of government subsidizing journalism. Should it matter if it's state or federal?
But the crux of the issue is the question "does a small amount of federal money influence NPR". I think the answer is "it does not". I've listened to NPR and read NYT, WSJ, WashPo for years and I've never heard a peep about the federal money influencing NPR.
The OP is stating there are strings attached and NPR answers to the Feds. I've never seen one iota of that in my entire life.