In the trolley example, you aren't choosing to actively cause harm to someone for the sake of the benefit of others. The trolley is going to kill someone. You may, at best, act to reduce the harm done by a process out of your control.

Where the torture example is concerned, one choice involves the active, intentional infliction of pain on someone for the purpose of extracting information that can be used to save lives.

In general, a fairly important principle in ethics is the principle of double effect. I.e.,

1. the action must be in itself good or neutral

2. the action's good effect must be intended, not its evil effect

3. the action's good effect must not be produced by means of the evil effect

4. the action's evil effect must not exceed the good effect in degree