Whether you book a flight with an online travel agency like Expedia, Kayak, etc or even for example through the Chase or Amex travel portals, you earn miles on these flights. You earn miles, even though you did not book these flights directly with the airlines.
However, the story is different when you book hotels through an online retailer. For example, Marriott’s terms state that “rooms booked via third party online retailers, like Expedia.com, Travelocity.com, Hotels.com, Booking.com, and Priceline.com, are not a “qualifying stay” and therefore are ineligible to receive points and miles for the stay.” Most of the other hotel loyalty programs have similar requirements. This limitation is true even when you books stays through the Chase, Amex, etc, travel portals as well. Although there have been some reports of people still earning their hotel loyalty points when booking through Amex and Chase. I guess just don’t rely on earning the points, is the best advice I can give.
Just something to keep in mind when you are booking your hotel stays.