Not all costs are fixed. Dealing with fraud, for example, becomes more costly with higher transaction values.
They will buy stuff that's expensive. This means that to credit card companies, the bigger the transaction, the more likely that they will have to spend time and effort on fraud investigations etc.
Man hours are expensive though, and as such it is important someone pays for it. And well, that's where the percentage system comes from.
Although they will sometimes do that as a test before making a bigger purchase. When my mother's card was cloned, the first fraudulent purchase was a coffee or sandwich at a railway station in a different city (but one close enough that it was believable she might have been there). Her bank only alerted her the next day when it was used to buy jewelry.