Why does Bitcoin screen dust transactions?

[laredotornado]

Given that users can submit a transaction fee with their transaction and miners can select which transactions to include in a block, why was the output size of version 0.8.2 of Bitcoin rigged so that "dust" transactions (those with an output size of 5.46uBTC) would be weeded out? I mean, if the transactions were too small, wouldn't miners just avoid them altogether? Why hard-code an amount?

This question is motivated primarily by the fact that when the Bitcoin price is high, that minimum transaction fee seems also high when converted to dollars.

- Dave