We've discussed this idea on the forums to the ground already and here is the overall summary of it.
Listing fees deter RE-LISTING not INITIAL UNDERCUTTING.
There is a large difference between the two.
People will undercut you regardless. The fees deter people from relisting because it costs them gil.
This gives player with large commodities an ability to knock out competitors by undercutting and forcing you to sell at a loss. If you don't re-list you face total loss. If you re-list you face smaller losses. Because these players have huge commodities of goods they can sit at lower prices and still make gil.
We see this in world of warcraft all the time. One guy undercuts 10 seperate players until hes the lowest and now holds the market. Everyone above him either has to relist at a loss or totally leave the market in hopes that player leaves that market which rarely happens.