If you want a really good read about what it was like in 1879 and what we've lost:
From the Cornell University "Making of America Project", a destination article about the fabulous Grayling fishing in Northern Michigan, for Scribners in 1879. The whole article is linked from the image above.
A determined and serious effort was undertaken to re-introduce Thymallus in the late 80's and early 90's - statewide, and it failed.
I don't beleive it can be conclusively said why the fish disappeared, beyond of course overfishing, destructive logging practices and introduction of exotics.
For me, this is what I think:
When the glaciers receded from Michigan 13000 years a relict population of grayling found a niche, that was allowed to gently and gradually evolve to fit an ecosystem that was unique, for them. This subspecies perfectly fit the rivers and streams that it had evolved into. Due to all of the above reasons, which simultaneously coincided with the widespread settling of Europeans in the area the fish didn't stand a chance. It was an ineffable expression of chance and evolution that is now gone - but maybe not for good.
At least with coming of the next ice age, which some say is imminent, the mile thick sheets of ice will come down from the artic in the next 5000 years or so, pushing the grayling in front of it, bringing it back to Michigan.
In 1920 on the Otter river in the U.P. an angler caught the same Grayling three times, and then no more, that was the end. That was less than 100 years ago.
So, the Michigan grayling is gone, but I think it is coming back. Maybe next time... things will be different.