I'm sure the engineers as Yahoo who actually created these patents got compensated, with the understanding (written though probably not verbally) that the patents were no longer theirs and the buyer could do what they want with them.
I was very conflicted about signing on as a co-inventor since I had strong feelings about software patents (and have even stronger ones now), but I was verbally assured that the patent would only be used as part of a defensive portfolio, etc., etc.
Later I was asked to participate in several other patents, and I declined. I wish I had declined to participate in the first one too, since it's now on the auction block and will very possibly be bought by a patent troll, making me complicit in whatever horrible things that troll chooses to do with my patent.
I quit my job at Yahoo when they sued Facebook. My patent wasn't one of the ones involved in the lawsuit, but the fact that it could have been horrified me, and I couldn't stomach the thought of working there anymore, even though I loved my job.
It irked me mostly because, sadly, many people still think that an issued patent actually reflects something substantive about the "inventor". So now I don't get to say that I'm the author of several patents on my resume, whereas the next guy might.
I took a patent law course and _hated_ it. My professor was once an interim director of the USPTO, and was rabidly pro-patent. That was annoying. There were also several patent examiners in my class, including two who examined software patents. One of those examiners agreed with me that software patents are generally bogus[2], but his job was to follow the law, and specifically the law as interpreted by the USPTO.
[1] I use scare quotes around inventor because like many software engineers most things seem obvious to me. Necessity is the mother of invention, not genius. And necessity will find you if you're in a competitive market, so you rarely need the prospect of a government monopoly to incentive you to "invent". Losing market share is usually all the incentive you need. (And there's nearly USD $100 trillion dollars in liquid or readily liquid assets in the world today. And while only a small fraction of that amount is likely to seek risky investments, it's still more than any entrepreneur would have imagined in their wildest dreams a few short decades ago. So guaranteeing returns on risky capital investments is a poor justification for government-enforced monopolies.) But FWIW in the relevant cases I both independently formulated the original ideas and wrote the implementations.
[2] Bogus for various reasons. But the whole "software patents are patents on math" argument widely shared in the FOSS community is pretty non-sensical in the patent realm. Patents are intrinsically about drawing difficult and arbitrary lines between the abstract and functional, and there are many dimensions where such lines are drawn. So expect examiners and lawyers to pretty much roll their eyes if you try to bring that up. The arguments against software patents that find the most purchase in the legal community are difficult to decipher without reference to concepts internal to the patent realm. The patent regime, like Catholicism, is based on a logic all its own. Internally consistent and analytically rigorous, yes, but ultimately divorced from reality.
Typically, about $1500 - $2000 per patent granted.