First, there's the bags that would need to be checked on any flight. Either because of their size or the total number of carry ones if yook all your bags on-board. These are subject to the bag fees (not that I'm agreeing with bag fees). The size, weight and number of your bags is under your control.

Then there are the bags that need to be checked for this flight for whatever operational need. IE: a Regional Jet with small overheads or a main-line jet whose bins have already been filled (I'm not getting into the topic of bin-hogs here). The lack of bin space for your (otherwise bin-friendly) bag is out of your control. The airline will check these bags for free.

Steve