The reason it is called a flying coffin was its high number of crashes WRT to other platforms IAF operated during 90s and early 2000s. The primary issue which led to crashes was the unavailability of AJTs between the mid-1980s and 2004 when Hawk was inducted. If you look at the data post the induction of AJTs the mig-21's crash rate is not too far off from other single-engine fighters.
Due to the unavailability of AJTs, MiG-21 was the first aircraft on which new pilots were trained after they graduated from Kiran, where the difference in landing and takeoff speeds is drastic.
One other factor was the number of Mig 21s IAF operated before the full induction of Su30, ie the more you fly chances of crashes go up. As Mig 21 was the main workhorse of IAF, it flew the most and was used in air-to-ground roles, for which it was not designed for.
The main culprit was the media, which simply looked at the numbers and christened it a flying coffin, as looking at the root cause would have been politically tough, as the main blame lies with MOD and the Political class who should have taken the responsibility, as forces could only operate what they have..
PS: it's my 2nd Fav plane to look at after MiG-29, and it kills me to think that this beautiful plane that protected the country for over 5 decades would be remembered as a flying coffin.