Not every anime hero actually looks the part. In fact, there are plenty of menacing anime heroes who look straight up villainous.
Sometimes, this is because they have anti-hero tendencies, and the character designers were trying to imply that through visual cues. This is definitely the case for Hiei from Yu Yu Hakusho, a former criminal who is still largely on his own team, but frequently works to protect humans and demons alike from danger. But sometimes, these types of characters defy expectations about what a hero should look like. Sajin Komamura of Bleach may look like a menacing wolfman, but he's actually a gentle soul.
Anime heroes who look like villains can take some getting used to, but they add to the overall visual experience of the series in which they appear.
Ken Kaneki begins Tokyo Ghoul with an innocent personality and an innocent appearance. After experiencing horrific violence, he becomes jaded and more willing to harm others in order to protect himself. Though he never quite becomes a villain, his looks take a turn for the menacing.
Gang Orca is actually a professional hero, but because of his terrifying appearance, he often moonlights as a practice villain for heroes-in-training.
Yes, the guy with the cow skull for a head who is holding girl by a chain around her neck is actually a relatively good guy. Elias Ainsworth dedicates his life to teaching others magic and protecting his community from magical attacks. He just looks creepy as heck while doing it.