I think some folks believe that some forms of macro algae need some of the waste/nutrients that the skimmer removes in order to grow well.
Some folks may feel that having both can be counter productive, and that the skimmer may be removing some of the trace elements and plankton along with some of the dissolved organics.
That the corals, bugs and inverts that feed on the plankton are better off without the use of a skimmer and that dosing foods for filter feeders is another expense.