Well, Ultimate Kuuga is meant to look like it might not be a good thing. The red eyes look more heroic than black eyes, but it still doesn't look friendly.
Not sure about the black Superman costume, but I remember in one of the animated DC movies, Jimmy or somebody else thought he looked like trouble. And Death of Superman was in the 90s anyway, which was apparently a time when comics tried really hard to be edgy.
Yet, I think the Garo armor (well, Kouga's version. His dad had unfriendly red eyes, and I haven't actually watched season 3, so I'm not completely sure about Ryuga's) looks perfectly heroic, even with the spikes and perpetual snarl. But that's probably because Garo is its own franchise, so I try to view it as having a different aesthetic philosophy.
Heroes that don't look blatantly heroic bugs me more in Ultraman, since the costume designs tend to make moral alignment somewhat obvious.