People are charged extra for heavier luggage because it is heavier than the baggage weight limits that have been set by the airlines themselves. When bags are over the limit, they get to collect a fee (and as we are all aware, fees have not always been included in the ticket price so they could compete for business yet still collect their money). It should be noted that they don't always charge; it's discretionary. When I flew first class, my bags were 25lbs over the limit and they were checked in without extra fees. But when I flew regular class and my suitcase was a mere 2 lbs over the limit, I was told I'd have to pay a $25 fee. I removed a blanket from the suitcase, bringing the weight down and eliminating the fee. I then carried the blanket onboard with me. If the exact same amount of weight was allowed onto the plane then it can't have really been about the safety.
It's not that I think total weight is not a factor, I actually do, I just think that in these circumstances it is not about the safety of the machine but instead about making money. Perhaps they had to change weight limits on baggage because the extra seats they've installed have used up the excess allowance - who knows. I'd really like to see the research behind their chosen limits because I'm guessing it was more about "average people pack this amount for a holiday so if we make is slightly under we can charge extra".
Airlines are in this to make money but if they raise ticket prices for everyone, there is backlash. Yet if they raise it for just a few (via specialized fees), then the majority won't take issue because these changes don't apply to them. Those who only take carry-on didn't blink when baggage costs were first applied. But then when the number of bags they could carry on were reduced, outcry. When the weight of carry-on was limited, further outcry. Then people adjusted and started to carry less, and now the airlines are searching for other means by which they can collect fees.