After reading the posts on this thread it appears as though the reason we are all so dumbfounded by the FIA's actions is that there is we are confusing the distinction between the rules of F1 and the rules of business. "F1 rules" are in place to enforce competition and a level playing field for all teams. Without making qualitative judgments I think it is fair to say that if a sporting rule comes in gross violation of one of the "rules of business" than the aforementioned sporting rule will be bent.
F1 could heavily penalize RBR, STR and SA teams, however they would do so out the peril or destroying F1 brand value. Unfortunately those of us who love F1 (hence we take the time to post on this web-site) are not the individuals the F1 management is concerned about. We represent no growth potential for the sport as we are already hopelessly addicted and our loyalty is unconditional. What they care about is growing the value of the brand, which means expending the scope and scale of F1. My thought is if they penalized these teams as a whole the field would be less competitive. And we can debate until that issue until the end of time, but for the sake of argument lets just suppose that is the case. That being said one of the main detractors of f1 (the outsider's view, not nesisarily mine) is that the top one or two teams dominate, and the field as a whole is not that competitive. So in this situation their is a choice to be made, do we rigidly uphold our sporting rules or do we bend under preassure. As such if the perceived cost of enforcing a rule exceeds the expected benefit, the rule will be bent every time.
These are just my opinions. In addition I am not saying that this is the way it should be, but merely how I think it works. In the end economics seem to govern most situations.