Hi Joe and welcome to the forum
Shipping costs is something that has to be covered somewhere, wether within the price of the item or as a stand alone shipping price. When you ay that you're heard it's a bad idea to over charge on shipping, that's absolutely correct. Even if someone accepts the over charge, they will often sting you on the feedback.
Of course over charging means just that, charging more than the shipping actually costs. If you are pricing your shipping at your cost, then that isn't over charging.