its an "open" cup- So theoretically, any team can participate ( think golf- US Open- where an amateur can qualify and play next to Phil ) - so long as they belong to a Pro League ( See below pyramid - so any team from first 4 levels are eligible )
Now, i just read that the reason, if correct, makes a bit more sense. MLS teams were looking to field their MLS NEXT ( aka reserve team ) INSTEAD of their full Pro level ( "first team ) roster.
MLS apparently wanted to open more "match dates" in season- ( read: more gate revenue ) as opposed to playing the Rochester Rhinos in a 2500 seat field.