In his second book the Way of the Wiseguy (?not sure if that's the exact title) Pistone talks about just this problem. Each captain or boss sets his own rules and they usually aren't that sympathetic to underlings' problems.
As Pistone tells it this runs downhill and so then the captains will tighten the screws on the soldiers who do the same thing to the associates.

In general this means that the guy on the street-the low level soldier or associate who may not have a crew of his own to shake down is always looking for new scams, new businesses, new ways to get out of spending his own money.

I think some bosses/capos use a set dollar amt /per week just to keep the accounting simple and guarantee they're getting what they think is a significant taste. In the example you give I think that soldier would be wise to give his captain the $2500 no matter what and then find other ways to make up the loss.