Considering I'm not very empathetic to corporations, I actually can see really great reasons from a not-a-company perspective why it would have been great if the companies had to pay. Not because I think companies should have to foot the bill for complying with something massively immoral and not because the U.S. is that strapped for cash (because I'll happily agree with you that it's chump change).
If the companies had been required to pay, there is about 0% chance we would have had to wait for Snowden to leak in order for us to find out about it. Given all those companies involved, I bet at least one CEO would have stood up and said "Nope, not gonna" very loudly and said what they wouldn't do and why with a strong streak of faux principles. Even if it meant that some CEO went to minimum security prison for a long long time.
Those payouts really amount to hush money.
All that said, I'm not surprised they got something and given the large scale, I'm not surprised it was cash. If it was just one or two companies, we might have seen some more elaborate, less accounting-friendly scheme.
I'm not incensed exactly but it's always a bit galling to pay for the rope used to hang you. Even if it's a pittance.