Fixed fees make bots performing micro-transactions untenable. Blending it with a percent fee is easy enough (x%, minimum of y BTC)
That lets you marginalize the impact of bots flooding your engine (GOXXED) by making it much more expensive (and thus, less likely) for manipulators to flood your market.
Good point. Though, I'd like to keep things as simple as possible - as a customer, I'm annoyed when I see a fee structure such as "0.20%, minimum of 9 EUR" (which is the starting fee of nordnet.fi, a Finnish stock trading firm), because I feel that I'm being unjustly punished for small transactions, and I feel the need to calculate the point after which I'm "not being cheated" any more (in this case, 9 EUR / 0.20% = 4500 EUR). That's just a hassle. Perhaps not such a big hassle with smaller transactions, but a hassle nonetheless.
How about just having a minimum order quantity, which effectively guarantees a minimum fee? For instance, a transaction fee of 0.5% and a minimum order quantity of 0.1 BTC would guarantee a minimum of 0.0005 BTC / transaction, which will probably be a big enough to prevent bots from overwhelming the exchange with orders.
Then again, the exchange should definitely be prepared to be overwhelmed.