I notice that this question glosses over the fact that the question-rep change was implemented at the same time as another significant change, which effectively raised the daily rep cap for users who received a lot of accepts/bounties (i.e. the users who actually provided the most help to others).
To claim that one change should been forward-only implies that all changes should have been forward-only, and I am fairly certain that those who were prone to receiving 200pt bounties or a half-dozen accept votes at 8 AM would disagree.
It would be interesting to see statistics on what percentage of users (especially high-rep users) actually lost rep as a result. The reams of questions being asked on MSO give an impression of widespread resentment which I think is misleading, because the group is self-selecting; few people are going to come to Meta to complain that their rep went up overnight. And I'm willing to wager that the vast majority of high-rep users, especially users over 10k, actually gained rep as a result of this change, because to get that high they generally would have had to provide a lot of good answers.
Several people are classifying this as a unilateral change to the rules, but to me, it's more like fixing a long-standing problem with the rep system. I'm not saying that people don't deserve anything for working to make their questions as clear and concise as possible, and neither is Jeff - the votes still count - just not for as much as they used to. This seems a lot more fair to the people who took their time to help other people, rather than ask for help.
What really makes SO shine, IMHO, is the quality of the answers, not the questions. Yes, there are some notable questions, but you can find questions anywhere. You can ask questions anywhere. What you can't do is expect a solid answer in 5 minutes. That's what's important on SO, that's the reason for asking a question in the first place, and that is precisely why the system should encourage people to craft good answers and reward good answers.
Question upvotes should never have been lumped in with answer upvotes in the first place. This should be reflected in the current rep scores, not just future ones. Part of the rationale for this change, as I understand it, was to reassess the "trust" of users who haven't demonstrated exceptional proficiency by virtue of their answers. Which is not to say that they aren't proficient; just that they haven't proven it.
So yes, applying the change retroactively is "fair." It is, in my opinion, making an unfair system fair. This may have inadvertently punished a small handful of users who were using their rep privileges effectively, but if you want to make an omelet, you have to break a few eggs.
Besides, the debate over question rep is almost as old as the site itself. It's disingenuous to claim that you had no warning.