I recently tried to use Expedia to book a flight from Vancouver to Toronto on Porter Airlines because then I could use my TD Reward points.
The default prices that showed up in the results looked the same on Expedia or directly on Porter, so it didn't seem like I was losing anything.
Except that base flight included no carry-on and no checked-baggage, which I needed to do. On Porter directly fixing that cost an extra $40. Expedia said it cost $60.
For this particular flight I also needed to be able to make changes after booking. On Porter that increased the cost by $100. On Expedia, $150.
I still did it, cuz, y'know - points. But I shook my fist at Expedia the entire time.