I definitely sympathize that you lost a booking over this. That sucks.
I can't speak on Vrbo's (Expedia) behalf but I suspect it boils down to economics and demand. I know from my own experience for my own business, we don't take Discover because they charge a higher rate to the merchant. Most Discover cardholders keep a Visa or MasterCard branded card and I've always had the client swap cards with no issue (Discover cardholders are used to it).
So I can only surmise that Expedia/Vrbo has not (yet) found that the potentially extra cost to accept Discover is outweighing the actual lost bookings that they (we) may be incurring. When/if that ratio flips, they will likely begin to take Discover...