People are seeing it very clearly. You, apparently, do not. They're not arguing about who gets the money (it all goes to SWA). It's the fact that instead of an integrated network and reservation system that allows a passenger to fly one leg on SW and another on AT, you will still be operating as two separate (and, in a way, competing) airlines. No exactly what a merger (or acquisition) is supposed to provide.

Ie, a passenger wants to go from A to B. There are no direct flights. AT flies from A to C and SW flies from C to B. They won't be able to book it, so they'll go to DL/UA/AA/US. That's lost revenue for you.

Are you seeing it now?