I have seen mixed reactions and I can't really tell if it's good or bad at this time, it all depends on how it works out in reality.
If a single $5,000 license allows you to operate in all states and territories of the U.S. it's fair enough IMO.
No, the $5,000 is a non-refundable application fee. I'm not certain what the license itself costs, but someone said it might be $50 thousand. Also, I think it only covers New York and you would need a separate money transmitter license from each state to do big business over the whole USA.
Section 200.5 Application fees
As part of an application for licensing under this Part, each applicant must submit an initial application fee, in
the amount of five thousand dollars, to cover the cost of processing the application, reviewing application
materials, and investigating the financial condition and responsibility, financial and business experience, and
character and general fitness of the applicant. If the application is denied or withdrawn, such fee shall not be
refunded. Each Licensee may be required to pay fees to the Department to process additional applications
related to the license.
I gather that essentially it acts as a legally enforceable mechanism to have exchanges that fall under this license operate ethically and transparently. I'll also refrain from posting the full text , it being 44 pages long - it's easy to click on the link and to read it without the need to clog this thread with pages of text. 
