Alt-X will activate the option to dot map which is what you did on accident. Having done that left click lays down a new dot, right clicking a previously created dot will remove it. Then hit Alt-X again to turn the function off.
Personally I find it extremely useful when trying to decide whether I like one spot over another, especially if I know I'll be overlapping big fat crosses. Yes it is not that hard to do it mentally, but being able to have a visual speeds up the decision making process. I'll often leave the crosses there until I do settle. It also serves as a visual warning sign if another civ settles nearby, that that city plot may either be less attractive or eliminated entirely.