Well, I'm just going to rehash what's in the link, but the banks had already been "rescued" to the tune of $1.2 trillion, with a Fed guarantee of $7.77 trillion BEFORE Congress was lobbied for TARP.
The government made back a small portion of the total output to banks throughout the financial crisis, not close to 100%, and then proceeded to further deregulate since the bailout.
At least some of those big numbers are overnight loans that were granted in exchange for collateral (i.e., they were secured by some asset or another) and paid back the next day.
That doesn't meet 'not paid back'. You can probably call it unfair.
I don't know the timeline of it, but the fed published a bunch of the data on one of the facilities here:
Note that on that page, it says All loans extended under this facility were repaid in full, with interest, in accordance with the terms of the facility.
The Bloomberg articles don't really talk about where the numbers come from, but I expect most of the other loans were similar, short term and secured by assets.
The government made back a small portion of the total output to banks throughout the financial crisis, not close to 100%, and then proceeded to further deregulate since the bailout.