You brought up the issue of cougars being part of the natural state, however, the natural state that they belonged in ceased to exist in most of the Midwest by the time of the Civil War. I don't think that many folks have a problem with a few well managed (again, not a natural state) cougars in isolated areas. However, the ultimate danger is having them get out of hand in areas with significant human/livestock populations like they have in parts of California where theymost certainly have beena confirmed threat to humans. There is also the issue that as a cougar population rises, they may start to figure out that cows, sheep, etc are much easier to catch than deer. As it stands now, most reports of cougars in the Midwest seem to be largely single animals passing thru a large area. However, if you start getting somewhat sedentary breeding populations, then the scenario changes dramatically.
A lot of things can happen if you have any more than a few cougars in some isolated areasof Midwest and most of them are bad.