It's not the sites themselves -- for the most past Hotwire, Priceline, etc. do a good job. However, it seems like a memo has gone out to every rental car agency and hotel that sells discounted cars and rooms to these sites to treat people booking via these sites like second-class citizens, which creates enormous badwill. There's a big missed opportunity here.
Let me give you an example: the cheapest rental car I could find for a recent trip of the type I wanted was $98.00 per day, but the price on Hotwire for the same class of car was $28.00 per day. What did I give up for the $28.00? Well, I gave up the convenience of going directly to my car off the bus, potentially getting a nicer vehicle via a free upgrade, and that's about it. What did I get in return? A reminder from the check-in person not less than 3 times that I had rented via Hotwire, a warning that I would be charged $120 for the vehicle if I brought it back even 1 minute after the return time I punched into Hotwire when I rented it (tip: on Hotwire, make your return time the same time as your flight time to ensure this doesn't happen to you), 2 attempts to try and upgrade me to a "premium" vehicle, and a 5 minute lecture on why I should be accepting the insurance because, get this, Hotwire doesn't provide me any protection (I've never had a rental car company offer me any free protection in all of the years that I've been renting cars).
Here's another example: I rented a room from Hotels.com for $98.00 and on the website for the same hotel, rooms were going for $210.00. For this particular hotel chain I happen to have pretty high status, but the person at the desk unapologetically informed me that because I booked with Hotels.com, they would not recognize my status, I would not receive any points for the stay, and I would receive none of the amenities (normally consisting of a couple of bottles of water and a bag of pretzels) that I normally get in my room. The really interesting thing was that their computer system had obviously correlated between my Hotels.com reservation and my chain profile -- I know this because the aforementioned statements were made preemptively before I even asked.
The discount travel sites are not to blame for this behavior, the rental car companies and hotels are. After all, the rental car companies and hotels are the ones giving the inventory to the sites to sell -- goes back to that old saying: "If you don't want them to buy, then don't sell." Unfortunately, the rental car companies and hotel chains are not only allowing this behavior from their employees, but it really appears as though they are encouraging the behavior. However, the end result for someone like me is that when I go to choose a rental car company or hotel chain to affiliate myself with and/or give the majority of my business, I'm not going to choose one that treated me like a criminal for purchasing through a discount travel site.
Of course, the rental car companies and hotels could turn this around. They could view each person that walks in the door as a potential lifetime customer of the brand and treat them as well as a loyal purchaser. Instead of being upset or encouraging their employees to be upset about a customer not booking directly, they could decide not to care what the purchase vector was and simply treat the customer like a customer. One key portion of this to ensure that customers, especially recurring customers, are booking directly would be to give them access to the same rates as the discount travel sites and/or be willing to match the price on the discount travel site (note: the only chain that I've known that will do this is Starwood, but you have to call the 800 number and tell them the price that a discount site is quoting -- in most cases they will match or get very close to the same price).
Remember when loyal customers used to be the most rewarded for their business by receiving the best pricing and service? There needs to be a shift back to these practices.