I could never figure out what the big deal was either. A card is a card!
But some people, including me, like to leave as much of their cash, debit cards, credit cards, etc. in the room safe and travel lightly in the parks. It's hard to get much lighter than a single room key. Also, being the victim of a stolen wallet in WDW once, I would give anything to be able to turn back the clock on that day and choose to put my wallet, credit cards, etc. in the room safe and just take the room key instead. If I'd just had my room key stolen, I could have made one visit to Guest Services, or made one call to the resort to have that key "erased." As it was, I had to cancel all my credit cards, my debit card, had to call the three credit bureaus and put watches on my credit files, and pretty much had a stressful and miserable rest of the day. Fortunately, the wallet was later found in one of the All Stars resorts (it was stolen in MK), with everything still in it except the cash. I was lucky, but still wish I had just taken my room key alone.
OP: yes, you can only have one CC# on file per ressie, but as one poster suggested, you can settle the final bill however you wish, with cash, credit cards, debit cards, or any mixture of the above.