I don't claim to know if the same applies in NL or semi pro football, but I would imagine every professional club wold have 'some' players on their books that earn significantly more than the manager and the bigger the team the more it will probably occur.
Most professional players have a tangible worth in the transfer market and I would assume that could be the main reason, and wherever you look it could be argued that some players worth in regards to contribution to the team and more who will probably be listed on the stock market or Companies House as a company asset, is more valuable.
Even Ferguson who must have surely been the leagues highest paid manager wouldn't have earned as much as say Rooney or RVP and Van Gaal not as much as his recent arrivals. You can debate the logic behind it, but no managers command £40m transfer fees and even if they walk out of their contracts and straight into another job in doing so, the club they desert invariably only gets contract compensation or at best a couple of million in mutually agreed compensation.
Fascinating question though