Hmm yea, you do have a point.
I admit I got a bit carried away on the barcode idea, mostly because I have used it at the airport and liked it. But I have to agree it might not scale as well to public transport use - the whole running after train thing.
Well, I guess we can meet in the middle and agree that NFC would be the near-optimal solution, when and if implemented securely (however unlikely that is.. ;-) ).