"To waive the fee" means to decide not to charge someone the money they would normally have to pay for a particular service or product. Full definition
Two cards will even waive the fee for two checked bags. (upgradedpoints.com)
That could make it easier to reach higher tiers and even waive some fees on award redemptions, which don't normally earn miles themselves. (travelcodex.com)
Some carriers will even waive the fee if you have elite status. (rewardexpert.com)