The tomahawk is a good airplane, if flown within limitations. The biggest concern with the airplane is that it was never certified. It's not just some minor changes to wing ribs and a change in the spar weight. The airplane was certified with a different airfoil; a completely different wing. Under that certification, I believe it was the only airplane to get by with such a crucial design change.
That is not the reason for it's reputation, however. Both the skipper and the tomahawk appear similiar externally, and both are susceptable to certain deep stall characteristics, to a degree. However, the two are different airplanes.
The tomahawk is not rigid under a load. It is also as a result, not consistant. One may spin the airplane three hundred times with full consistancy, or six hundred for that matter. But somewhere in there, perhaps on the 601st, it becomes uncontrollable; it won't recover. It buffets and oil cans, and the empennage flexes, giving a slightly different aerdynamic effect; it becomes a different airplane.
Part of the bad reputation is not deserved. There are a lot of tomahawks around the country in constant, active use in the training arena, and as personal rides. Airplanes that are constantly put into stalls and spins are perhaps more likely to be involved in accidents related to aerial maneuvering, or recovery issues, and that may be part of the issue.
The following site addresses some of the concerns, recommends specific further testing, and has a brief bibliography with references to further pursue the matter.
http://www.unomaha.edu/~unoai/avn8120/Resources/jmccaberp.html
The following Air Safety Foundation tends to disagree with much of the controversy, and is worth reading:
http://www.aopa.org/asf/asfarticles/t-hawk.html
http://www.aopa.org/asf/asfarticles/t-hawk.html