I just want to highlight the point that ehallison, Flying Lawyer, and UKtravelbear all mentioned earlier. You're not getting frequent traveler benefits because of a decision your employer made. If you choose to be annoyed, it really should be with your employer.

Being for-profit businesses, hotels need to limit costs to make money. In most cases, when someone books through a third-party company like Expedia, the hotel must pay a commission to that company. All of the major US hotel chains have decided that individual hotels don't have to pay that commission and pay the costs associated with providing frequent traveler benefits. Hotels will pay one or the other.