Surely the issue is not whether a city is a capital, a regional centre or whatever but its ability to provide both inbound or outbound passengers in sufficient numbers in all cabins to make a decent profit - Canbera is a capital but the magnet in that part of Australia is Sydney, similarly Madrid is a capital but other spanish cities do nearly as well (sun, sea and sand).
Surely the issue for Manchester is, for regional routes, Liverpool nearby, and, as has been said, no airline or alliance using it as a hub? In addition, the fast train to London must be becoming more and more of an issue.