I fly (flew?) the London-Dundee route a few times a year.
Unfortunately, because of the length of the runway, larger planes could not land. (The airport authority wanted to lengthen the runway but the land on both sides is owned by the University of Dundee and they are not selling.) That's the reason it was never popular with other airlines.
Add to the fact the price of flying that route was not cheap.
Additionally, with the direct Dundee-Edinburgh airport coach service, most locals take it to the Airport. More flights in and out of Edinburgh and much cheaper ones. I've taken it.....just a longer process than a direct flight to Dundee. (And even longer if you take either the regular edinburgh to Dundee coach service or even the train.)
I'm in Dundee now and the future of the airport is under discussion. Besides Loganair, most of the air traffic was private aircraft landing for St. Andrews. Flying into Edinburgh or is the only other alternative then private transfer to St. Andrews. (People arriving in private jets are not concerned about saving money on the train/bus combination.)
There is talk of opening up Leuchars airport to commercial and private traffic as it is larger than Dundee Airport and closer to St. Andrews. It is currently a military field and closed to private aircraft.
BTW, Loganair has also announced the closing of its base in Southampton and has limited the number of scheduled flight from Inverness to the northern and western Scottish islands.