Its like anything else, you pay for a quality and affluent experience. That either appeals to you or it doesn't.
For instance, I enjoy shopping at Nordstrom. I like their clothes, suits, and the whole experience of shopping there. Last weekend I stumbled into a "Nordstrom Rack", Nordstrom's outlet if you will. I bought several things at great prices, a couple pairs of $150 Tommy Bahama slacks for $50. A few $80 shirts for $30. Now, the savings were great but the whole experience was like shopping at a swap meet. It left a lot to be desired.
So, I'll shop there from time to time but I'll still shop at the real Nordstrom.
Yeah you can do the work yourself but I enjoy the experience of having the car taken care of by the Lexus dealer, I get no hassle loaners (they're not "free", they're part of what you pay for with the service), I get dropoffs and pickups at my leisure. Plus, I have no desire to do maintenance myself and the car has a perfect Lexus dealer service history which is bound to make it easier to sell.
To each their own, but there are reasons people use the dealer.