A big part of the problem is that as patients, we observe single discrete outcomes.

For doctors an aggregate 1% chance is low, but the realization of the outcome in a single person is not a percentage, its binary bad side effects or not.

Admittedly, doctors could usually do better in communicating risks (e.g. see the famous example of 1/3 risk of impotence, which patients interpret either as 1 out of 3 people, 1 out of 3 times having sex, or 1/3 of the time of sex).