As the GAO report notes, one of the big reasons a profitable company wouldn't pay taxes is because of carried losses. This is an important concept so let's use an example.

Say you start a business. Like many businesses, you aren't profitable at first. In year one, you lose $100. Then in year two, you do you a bit better so you make $10. Now the government says you're profitable, and demands their 20% in taxes.

But hold on--you may notice that you haven't actually earned any profit. You're still down $90 from where you started, yet you're being taxed on "profit". The issue is that taxable income is reported in an arbitrary time period--it ignores all the money you may have lost in previous time periods. That's a big issue.

So broadly, there are a couple common ways governments can deal with this. Number one is to subsidize losses in the same way that they tax profits. However, giving large sums of money to corporations tends to go over poorly with voters, so most governments tend towards option two: carried losses. The basic idea is that you can carry past losses forward to offset future "profits". So you made a profit of $10 this year, but since you lost more than that last year, the government recognizes that you're still down money in total and doesn't tax you. Once your profits exceed the past losses, you start paying taxes. It can get quite a bit more complex in the real world, but that's the basic idea.

A lot of these companies that are being called "profitable" were really only profitable in a narrow, arbitrary period of time. They're still working to make up all the money they lost beforehand.

Of course, the GAO report notes that there are other reasons a profitable company may not pax taxes. Companies might have received deductions or tax credits for various reasons. It doesn't go into any detail assessing what factors contribute the most. We could have a detailed discussions about what tax credits make sense, and which don't.

But despite the outrage this article is obviously meant to provoke, the study it references really doesn't prove anything very outrageous. There are economically sound reasons a "profitable" company might not pay taxes. To the extent that it can be attributed to tax credits or deductions with more dubious logic, the study doesn't go into detail.