You cut out the middle man and you make more profits selling it directly from the factories. FTL and FNL pay a certain amount to Nike in order to sell, but it's still cheaper than MSRP. Nike can just straight up charge the MSRP and reap higher profits from selling a "hot" sneaker.
There was talks about this years ago that Nike was looking to cut out the brick and mortar stores from selling Js. Nike pretty much did all that except to the big chains and those rare mom and pops due to their location. Even then, they have lessened the stock to those stores regarding "more hyped" releases.