It's perfectly relevant when questioning whether or not the same scrutiny is applied to all players or if TfL are just trying to make headlines attacking the big fish.
I think it's reasonable to go after the people who essentially brag about breaking the rules. If you shine a light on your own questionable activities, don't be surprised by the consequences.
So the theoretical issue there is "why are TfL not applying their regulations to other companies", not "why are TfL applying their regulations to this one". If you have any evidence at all that TfL are licensing other companies which have similar questions around their ability to comply with regulations, I'm reasonably sure you could start a small movement around it.
Of course the same scrutiny is applied to all players. The fact that Uber chooses to respond by launching a petition, rather than attempting to comply with the regulation that every other minicab company in London complies with says much more about Uber than it does about TfL.