I don't think that the 5000$ fee was a the problem with BFX.
Please bear in mind this is only the non-refundable application fee. Still, if you spread that across all 50 states it would be a cool quarter million, right off the top.
It was estimated that staying compliant for a nationwide bitcoin business would cost roughly half a million dollars per year. You've got to keep a compliance officer on staff (or several, depending on the size of your operation) you've got to file your quota of suspicious activity reports, and of course you'll probably want to hire Lawsky's consulting firm, not because they'll help you remain compliant, but because they will know exactly which palms to grease to keep you on the good side of the regulators. Don't feel like retaining their services? Don't be surprised to be at the top of the list of random audits.
This whole banking regulatory system is a scam and it stinks to high heaven.