I know about the tragedy of the commons but let's just say that I've always been very skeptical about it, it really does not apply well to most real life scenarios. I understand what you're saying and maybe I'm the one who is clueless here but I'll try my best now to make sense of all of this.
In some cases tragedy of the commons is overcome when there are additional factors at play. It depends on the ratio between incentive to defect and the stabilizing forces.
But I think it's much more prevalent than you think. Voting is a classic example. AFAIK voting rates in US are very low, and it is generally agreed that the total welfare would increase if everyone voted (the total effort of all people voting is justified by the election of a party which better addresses people desires). But for each person, the effect of his own vote on his own welfare is negligible, so most people pass.
Another example is software. Would it not be better if instead of dealing with DRM, registration keys, closed platforms and so on, companies would allow anyone to download the software, specify a price, and receive payments on the honor system? If this was in place and everyone (who pay under the current system) paid, everyone would be better off. But everyone would be incentivized to spare himself this cost, which eventually results in the breakdown of this model and resorting to DRM. (Some people have offered software on an honor system, somewhat successfully, but mostly because of the novelty factor - it doesn't scale.)
There are no doubt cases where it could have occurred, if society hadn't been able to redefine the rules to dispel it.
People have been suggesting all sorts of factors that would mitigate the tragedy of the commons problem in Bitcoin mining, but I still doubt that they will be enough quantitatively. We need something about which we will be able to be much more confident.
I don't believe that high fee miners will defect to low fee pools simply because it appears that they would get more by going there. In fact they get significantly less because by doing that users don't have incentive to pay high fees anymore.
To think about this in another way is to imagine that all miners will defect to the low fee pools. What happens then? Mining becomes unprofitable and some miners will again attempt to raise fee thresholds.
Again, if I am a small miner, the effect of my mining on the equilibrium is negligible. By going to a high-fee pool, I'm increasing the frequency of high fees by about 0.0001% (which I will also enjoy). If I go to a low-fee pool with twice the total reward, I increase my rewards by 100%. I would much rather that all other miners go to the high-fee pool; but whether they do or don't, I'm still better off at the low-fee pool.
In other words: My personal benefit from defecting is always higher than my share of the global benefit of me cooperating. I lose from other people defecting, not from me defecting. (Unless I'm a sufficiently large miner.)
You need some balancing factors to prevent that from happening. And they need to be stronger than the total incentive to defect.