Let's talk about the National Bank!
So a central bank, which is essentially what this was, is an institution that manages the National common currency. But it also allows Americans to buy a portion of the federal debt to hold as bonds. These bonds are essential building blocks of industry as they allow large amounts of money to be traded in the form of mutually valuable liquid assets with no beef to fully liquidate hard or "real" assets like land or other property. Instead, you could borrow bonds leveraged against your property to make use of the value to take on new ventures.
This alleviated what was a major problem in the early American period where there were simply not enough real assets to facilitate meaningful ability of business interests to nimbly meet needs. It's how you have situations like the one New York faced where it desperately needed a water company but no one had the liquid assets to make one a reality until years down the line.
The central bank also backed a common currency - typically backed by a 'hard' currency asset such as silver or gold - that allowed for meaningful interstate commerce.
This was opposed by Jefferson and Madison because they felt that it was a waste of taxpayer money, had no constitutional mandate to exist, took power away from the state's by robbing them of their ability to manage their own monetary policy. Most importantly they felt it only benefitted wealthy New England and New York bankers and took money out of the pockets of "common people". It also had largely no nexus to agricultural business practices while costing taxpayer money which made it deeply unpopular in the South.
However once Jefferson took office, Madison and Treasury Secretary Albert Gallatin found the bank in practice did not actually cost the taxpayer very much at all while having fringe benefits that helped them manage their budget surplus into for example completely overhauling the Navy to fit Jefferson's new vision.
This has left people who opposed the bank on moral and legal grounds deeply skeptical of Madison who seemingly only opposed the bank on practical grounds, hence the 'secret federalist- label.