Thing is, it's not so much for those with lots of money. Here is the breakdown:
100 gil item, costs 105 gil.
1000 gil item costs 1050 gil.
10,000 gil item costs 10,500 gil.
100,000 gil item costs 104,000 gil.
1,000,000 gil item costs 1,004,000 gil.
Since it's up to a maximum of 4000 gil, it won't really have that big of an impact on players who have money, and those who don't. In fact, other MMOs (XI) for example, charged you for just putting items up for sale.
Now, one could argue that the charge was to the seller, but at the end of the day the buyer is the one who pays. All taxes, fees, etc trickle down to the buyer anyway, and thus the fee would only end up being invisible as the sellers would raise the prices in the end.
Anyway, when buying from the search it's a one time fee, that's optional. So if you want to save 5, 50, 500, or 4000 gil then by all means run, but just because you don't have millions of gil shouldn't stop you from using this feature. Heck, I figure if anything, players who have more money and who buy more things, if they want to Dave Ramsey it, will still run to save the extra change.
