Flights are fundamentally different than hotel nights. When you buy a flight through a travel agency the credit card transaction is still generated by the airline, with rare exceptions.
When you reserve a hotel room it can go either way. If you book a prepaid stay you are actually buying the night from the agency which has a made a bulk purchase, and you will be billed by the agency. Discover may (or may not) recognize it as a travel transaction. If you book a post paid stay you are merely making a reservation through the agency and the hotel will charge your card during the stay.
Your right, and it would be easier if Discover were giving the rebate on the broad "travel" classifications, most all online tavel sites can qualify. In this case the stricter subset of airlines and hotel classifications would require that it show up coded as Hotel purchase.
I have found that Discover CS is pretty good about helping if called on a technicality.
As a matter of fact, they will offer you extra cash back if asked about a promotion to get $1 per transaction...usually limited to 20 for a month, it may depend on usage. My wife recieved the offer last fall and I called and was given the same, by a CSR a few months later. $20 for a phone call is worth the effort...you could also ask them about the current promo details, and get their opinion