The existence of irrational numbers was dangerous.

The Earth being on an orbit was dangerous.

Non-royalty having legal rights was dangerous.

The prole having legal rights was dangerous.

The idea of electing any public officials was dangerous.

Women having the right to vote was dangerous.

Not invading foreign soil to extract their natural resources was dangerous.

All of these ideas were dangerous and had severe consequences at the time, some challenged scientific norms, some social norms and some effectively undermined the state. You don't get to look back at those ideas with your 2020 hindsight vision and declare they were harmless now because they were radical, revolutionary and terrifyingly dangerous ideas. Why else would the inquisition kill so many people?