A tower can only capture a meeple at a time.
As the rules say:
Whenever you place a tower floor, you may immediately take 1 meeple off the board
What would you like to clarify about The Flier and the Tower in particular? This situation about multiple meeples on a tile is not only linked to The Filer. There are several mechanics that allow you to place several meeples on one tile, or even the same feature depending on the mechanic:
* Using a magic portal (Exp. 3)
* Moving a wagon after scoring (Exp. 5)
* Deploying a meeple from Carcassonne (Exp. 6) - Does not matter if target feature is occupied (meeples are scored right a way, so the tower cannot affect them)
* Placing an acrobat (Exp. 10)
* Using a flying machine (Mini #1) - Does not matter if target feature is occupied
* Add a meeple with a crop circle (Mini #7)
* Using the Add a Meeple/Place a Meeple action (20th Anniversary expansion)
* Using Synod/Change Position gift (The Gifts) - Does not matter if target feature is occupied
* Placing a phantom as a second figure on a tile (The Phantom)
* Trapping a meeple by Solovei Razboynik/Vodyanoy (Russian Promos)