The min fee on low priority txs is ~1 US cent and the dust threshold is ~0.5 US cents. What small transaction market are you talking about?
Agreed. The low priority txs is still acceptable, but if bitcoins value was say $1000 USD then a fixed threshold would represent an ever escalating minimum fee.
Summary: The minimum fee needs to be adjustable and probably the best way to accomplish this is via an open market solution - let the miners who are processing the transactions set the fee.
Miners do set the fee and as a result the min dust threshold (54.3% of min fee). The min mandatory fee is simply a default and is used to protect the network from denial of service attacks. The default has been lowered four times in the history of Bitcoin to keep the min fee (on low priority txs there is no min fee on high priority txs) at a low level of around 1-3 US cents.