But that's an inherent bias, isn't it?
There's no question that Hojo did terrible things, was a terrible person, and clearly has a detestable temperament. However, that's only one facet of his personality. To the right person, or rather, a person adjacent or of a similar perspective of him, they're not as much a problem. One can argue the percentage that these negative traits take up of his total persona, but the simple fact remains that they are only a part of him, or at the very least, are multifaceted, especially to those who actually find value in these traits.
Which is not unheard of. People excuse all sorts of traits or behaviors in light of perceived positive traits.
Hojo is obsessive and driven by an insatiable lust for knowledge and research. For the outside viewer, with the gift of hindsight, it's clearly a negative trait, but to some like Lucrecia, President Shinra, the executive board and other Shinra scientists, they saw this as a strength of his.
Hojo would do whatever it took to get what he wanted, ethical or moral limits be damned. To Shinra and those close to him, this was acceptable and worthy of respect because the results were groundbreaking.
Hojo has a dark, witty and cutting sense of humor. He's intelligent, powerful, and willing to do whatever it takes for what interests him. It's really not that surprising Hojo would have people who saw these traits as not completely irredeemable as most would find, especially viewers with the hindsight of 20/20 hindsight and awareness to the overall plot. To those around him in Shinra, he's just an eccentric genius.
To the rest of the world, a madman who was dangerous and architect behind the darkness of Shinra.