RHorning I think you need to do some more reading up on transaction fees.
http://www.bitcoin.org/wiki/doku.php?id=transaction_fee is a good place to start.
Topic: Flood attack 0.00000001 BC is another thread worth reading.
If that is the case, I would argue that it should be stripped from the specification for all of the reasons suggested in the threads about deflation. It doesn't seem logical except strictly to stop a flood attack, and with the increase in value for Bitcoins I certainly can see the potential for when this would be a rather significant fee. At what point should this be moved to 0.001 bitcoins or something smaller?
It just seems like a very arbitrary value that was put into as a "magic number" that made sense only because at the time it was put into the code that it seemed like such a small value that nobody would reasonably be wanting to logically be sending money in denominations smaller than that amount. At least be logically consistent here when it is said that Bitcoins are "infinitely scalable" to any size of economy, and that at the same time it isn't.
A flood of transactions all from the same node, perhaps, ought to be charged transactions frees, or perhaps the whole system ought to be rethought. There are other solutions to this problem, and this seems like a temporary stop-gap solution that wasn't thought through all that well.
It really is fine for now, if it becomes an issue future clients will have a lower fee (if any). If you choose not to pay the fee the only thing that happens is that nodes who charge that much will not include your transaction in their blocks. Really, only one node needs to have that fee removed and sub-0.01 transaction will go through, although you'd have to wait until that system generates a block. So those super-small transactions would sit at 0/unconfirmed for a while, but once it got into a block every block after that would count toward it's confirmations.