1. It's a charity tax; you have to convince people to incur the cost of Tor (i.e. CAPTCHAs everywhere) for activities that don't require Tor.
2. You can't neutralise a poison by diluting it.
Firstly, from the operators' POV, if there's a widespread agreement that people use Tor even though they don't need to, then they know voluntary users can be pressured not to use Tor through sheer inconvenience. Even if you wanted to boycott a service that blocked Tor, it's notoriously hard to make good on that threat unless you wield a lot of power or annoyed a very large number of people. So the consequences are minor.
Secondly, the percentage of malicious Tor traffic is a red herring. What operators care about is the origins of malicious traffic. If 50% of your attacks come from one particular country (or Tor) and the cost of losing that traffic is less than the cost of that malicious traffic, there is a real incentive to block that traffic. Combined with the first point, the cost of losing voluntary Tor users is insignificant if they can easily choose not to use it.