Studies re: antioxidants show that large doses of isolated compounds are not so good for you. The famous vitamin E study is an example of this. Scientists decided to study vitamin E, though, because people whose diets were high in naturally-occurring vitamin E had improved mortality -- in particular, these diets were cardioprotective. A similar paradox is being seen, to a lesser degree, in comparing diets high in fish and diets that include fish oil supplements or omega-3 supplements.
The combination of studies shows not that "antioxidants are bad" but that we don't understand how to isolate their benefits. Diets high in antioxidants from whole foods (dead plants and animals), rather than nutraceuticals or supplements, are consistently linked with health. Apparently it's not so simple as isolating one compound -- we need a balance of chemical compounds coming in, working in concert.
(It's like we evolved to thrive on real food instead of pills! Weird!)