Pay is a driving factor in any game that expense is generated to continue normal operation. Covering operational costs should be the responsibility of the interested parties. For small scale operations this is true, larger scale starts leeching from the Fleet's larder.
A honor-bound general contract for Imperium members for their services would be helpful in setting ground rules for small scale operations. Perhaps there could be a contract council to decide rates of pay and resolve contract disputes. Larger operations would have their own set of rules considering the sanctioning of higher authority.
Also the Commander's Cut, say at 3% of total profit, should suffice in generating enough capital to make the Fleet's footprint grow when utilizing Fleet contracts. Consider using a higher tax rate for more Fleet intensive operations to cover ship, equipment, and cargo losses.
In a nutshell:
1) Small ops paid for by contract members with a small fee for Fleet, larger ops paid by contract members and Fleet with a larger fee rate.
2) General contract for Fleet members. Creation of a contract council. (More work for officers.)
3) 3% Profit Tax small scale ops. Variable rate for larger scale ops. (More Fleet involvement requires more Fleet investment.)
My two cents.