1) The chart doesn't break the fee amount down. 1 satoshi for a giant spammy piece of garbage going to lag your block and probably cause an orphan is more likely to be passed over than a free "normal" tx.
2) The chart doesn't break down required fees vs optional fees. tx with required fees (paying the absolute min) tend to be "junk" for lack of a better word.
Agree it would be useful to further break down the transactions by required vs. optional fees, or even shade them in some way to indicate how much above the minimum they are, if any.
3) The reason why free tx are punched up above 10 BTC is that the min fee rules require 1 Bitcoin - Day to avoid being considered low priority and thus require a fee. It would make sense that most large tx are not low priority (due to coin age rules) and thus don't need to include a fee.
Ah, this seems obvious now in retrospect. The bulk of the no-fee transactions confirmed right away are the higher amounts that exceed the low priority threshold. The no-fee transactions beyond a block or two do seem as spread out in value as the fee-paid ones.
TL/DR the chart is interesting but it needs a lot more stratification to draw any meaning.
Maybe I could get in touch with the site author and offer a small bounty to add more detailed analysis.