The Bureau of Transport Statistics has a number of customizable datatables that you can download. I created one covering all commercial international flights departing or arriving to the United States in 2016 (it only covers the first nine months). Then I manually selected all flights arriving from muslim majority countries. This is what I got:
|Country||City||Total flights to the US (Jan-Sep 2016)|
|United Arab Emirates||Abu Dhabi||1773|
|Total Muslim majority countries||14269|
There were flights from 21 cities in muslim majority countries, but eight of them had only one direct flight in the first nine months of 2016. That leaves only 13 cities with more than occasional flights to the USA. Ten of them are covered by the electronic device ban.
The three not included are Dakar (Senegal), Karachi (Pakistan), and Baku (Azerbaijan).
However, all flights from Dakar were operated by Delta and South African Airlines, not by national companies. Flights from Karachi, all arriving at JFK, were operated by Pakistan International Airlines (PIA), but apparently PIA now only flies to JFK via Manchester.
That would mean that the electronic device ban in practice includes all direct regular flights to the United States from Muslim majority countries operated by companies from those countries, except in the single case of flights from Baku to New York, which are operated by Azerbaijan Airlines. And it certainly covers all flights from Muslim countries in the MENA (Middle East and North Africa) region.
Thus, what has been presented as a case-by-case decision looks much more like a blanket ban for companies from Muslim majority countries. This reinforces the doubts about whether this is a security decision or something else.