Let's say you plan on selling your game for $20. Under today's operating standards, Valve's cut would be $6 and you get $14 for every game sold.
Under the new proposed changes, you are essentially pre-paying your cut to Valve, so for the first 833 games sold, you get 100% of the profits (and Valve's cut is the fee you paid originally). In this scenario you're still earning the same amount of money: $11,660 ($14 x 833) but are instead paying $5,000 up front and receiving $16,660 on the back end.
Of course these numbers scale depending on Valve's fee, number of sales, and the price of your game.
I think what people are arguing is that $5,000 doesn't seem like a lot of money when, if you have a viable product, you stand to gain much more money simply by virtue of having your product being sold on Steam. The only way you "lose" money in this scenario is if your $20 game fails to sell 833 copies, which I think to most casual observers is a pretty good metric to keep the shovelware from the store.