There are several ways you can protect your power armor. Some are more effective than others and I'll list them in increasing order of effectiveness (which approximately equates to difficulty/annoyance as well.)
- Remove the Fusion Core. This reduces the chances considerably, but is not a guarantee.
- Remove all the pieces of the armor as well, leaving just an empty frame. This mitigates if it does get stolen.
- Leave them some where remote or difficult to get to in the settlement.
- Leave them on a yellow rig. Often I have to move the suit away from the rig to get my companion to don it, settlers will be less inclined to don a suit that they can't get into.
- Create an inaccessible Suit Depo. Build a tall tower, and then deconstruct the stairs. Put your fast travel rug on top. Only way to get to the suits is to fast travel there, don armor, and then jump off.
- Keep your suits at an empty settlement. No beacon, anyone who shows up anyways send to another settlement.
However, there is only one way to guarantee the settlers don't take your power armor, and that's to put them in power armor yourself. ;)