Those who own publishing on the songs on radio do get paid (typically the songwriters unless they sold ownership).
Waters as the songwriter does get paid, but it's a royalty on aired music, which is not a sale. Anyway, royalties for radio can be paid by minute of airtime, not per song. Waters' contract with the publisher is per album, with the stipulation that no per song sale is allowed. Waters has no contract with stations regarding long his songs must be played. Royalties for internet radio and any other download is "per song". Waters wants all downloads and internet play to be per album, as per contract.