Just using your first example, an increase in marginal rate (above $1 mil) from 5% to 9%:
$2 million income (your example) :
$50,000 + $90,000 = $140,000, or 7% of total income , a 2% increase in the overall (not marginal) tax rate.
You'd never see an increase in the total tax rate, obviously, as the higher marginal tax rate doesn't apply your entire income.
You'd never see a 4% increase in the total tax rate, obviously, as the higher marginal tax rate doesn't apply your entire income.
Does that make sense?
I agree that the taxes paid are 140% of what you would have paid without the 4% increase in the top marginal rate.
A more accurate headline for this article would have said something along the lines of "a 3% increase in the top marginal rate". Assuming, of course, that is what's being proposed. It seems pretty likely, but the article is short on details.
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On edit:
This just a different way of looking at the same numbers. I know that's probably stating the obvious, for many here. The increase in taxes paid would certainly be of interest to the taxpayers affected, while the change in overall tax rate seems better for comparing the tax rate paid by various income level taxpayers.