Respect for autonomy means that you don't interfere with freely chosen, ethical actions of other people.
This means, for example, that you shouldn't kill others. Serious bodily injury, enslavement, incarceration, coercion, and suppression of rational faculties also violate autonomy when they interfere with freely chosen, ethical actions. Respect for autonomy can be more precisely defined by the following principles:
Principle of joint autonomy. You should not do anything that you are rationally constrained to believe is jointly incompatible with the freely chosen, ethical actions of a group of one or more other persons. Throwing a bomb into a crowded street violates autonomy, even if there is no one person you know will be harmed by the bomb, because you know that someone on the street will be harmed.
Principle of interference. Interfering with unethical behavior does not violate autonomy, because unethical behavior is not freely chosen action. It has no coherent rationale and therefore cannot be distinguished from behavior that is not deliberately chosen. For example, you can grab a mugger to prevent him from attacking a victim. However, the interference must not go so far as to prevent ethical action, unless there is implied consent (see next point). Also, the principle refers to interference by an individual, not necessarily by the state.
Principle of implied consent. You can interfere with a person's ethical action, without violating autonomy, when that person implicitly consents to a policy that is consistent with the interference. You can tackle a distracted pedestrian who is about to walk into oncoming traffic, because the pedestrian already has a policy of not walking into traffic and therefore implicitly consents. You can tie up a burglar who breaks into your house without violating autonomy, even though this constrains ethical as well as unethical behavior, if it is necessary to protect yourself. The burglar already has a policy of taking similar actions to protect himself and therefore gives implied consent to such a policy.
Principle of informed consent. You can expose a person or group of people to harm, without violating joint autonomy, when there is informed consent. You can administer a vaccine to 1000 people even if you know that it will make one of them ill, if all 1000 give informed consent.
For additional explanation, watch the video Rational choice II (or read the transcript). It is part of an online ethics tutorial that consists of the following 30-minute sessions: