So to put numbers to this, this is how I see the breakdown. Let's say my notional paycheck is $1000.
B/c I put, say, 2 exemptions, let's make it a nice round 10% tax bracket that's taken out each paycheck for "Federal Income Tax". That's $100.
Let's say I live in WA, so my state income tax = 0.
My FICA (since I make less that 106k /yr) is 7.65%, or $76.50.
So my net pay is $824.50, and I paid $76.50 for Social Security/Medicare/Medicaid and $100 in federal income tax (to pay for things like DoD, SS/M/M overruns, interest on the debt, etc). What the article was saying (and I think Denny and PapaG as well) is that 45% of people got that $100 per paycheck back. They had no Federal Income liability. You're correct that they still had to pay that $76.50, b/c that goes to SS/M/M (and they MAY have received a refund big enough to cover that, but I don't think that was the point of the article).
I think that the premise of the OP was that 45% of people are ending up paying $0 per year toward Federal Income Tax (to pay for DoD, SS/M/M overruns, debt interest, etc) and then a bunch of them saying "I'm satisfied with that!". Not "I paid $100 per paycheck, and on April 15 didn't have to pay a dime extra, and I'm satisfied with that!"
Someone pipe up if I'm way off here.