Disclosure: I work for financial institution in the US.
I think that the nature of wire transfers makes them somewhat risky. The institutions facilitating the transfers assume some of that risk for their consumers. If a large some of money is moved from your account to someone else's, and you dispute the transfer, the institution sending the wire may have to refund you the money.
The cost of a single transfer offsets the risk of the aggregation of fraudulent transfers. This could be a calculation of volume, fraud rates, average amount transferred on that channel, etc.
This is all in addition to network costs as payment processors (third party inbetween financial institutions)
Checks are a little different. Many banks will not allow immediate availability of funds with checks which allows banks some time to catch fraud. Many businesses also communicate their check registers to banks which prevent forged checks from clearing the bank account.
I think that the nature of wire transfers makes them somewhat risky. The institutions facilitating the transfers assume some of that risk for their consumers. If a large some of money is moved from your account to someone else's, and you dispute the transfer, the institution sending the wire may have to refund you the money.
The cost of a single transfer offsets the risk of the aggregation of fraudulent transfers. This could be a calculation of volume, fraud rates, average amount transferred on that channel, etc.
This is all in addition to network costs as payment processors (third party inbetween financial institutions)
So, fees = portion of network cost + risk offset
Hope this sheds a little light.