'I can't check you in without your reference number'!
This is the frequent refrain at check-in desks, particularly with no-frills airlines. Once I politely enquired if it wasn't at all possible to check me in with just my passport for a domestic flight on a no-frills carrier, to which the answer was an emphatic no. Well a fortnight later there was a monster long queue at check-in and the staff were clearly trying to check people in as fast as possible. Did they ask for my reference number when I presented my passport? No - rather the lady was happy to confirm from presenting my passport that I had a pre-allocated seat and had booked for hold luggage.
I am more than happy to present my reference number at check-in, hence why I carry it every week. Yes, I appreciate it's probably easy to have a standard method of checking people in. Just don't see why the check-in staff had to tell a porkie-pie in the first instance.
Bit of a difference when travelling BA/BMI domestic and all I take is my FF card - no passport/drivers license/reference number required or asked for.