I don't think anything you've written is a contradiction to R' Miller's points. As yitzgar points out, there's a big difference between taking out a lesson for klal yisroel as a whole and making cheshbonos about each individual. Of course there's a cheshbon for each individual as well - one that doesn't necessarily involve looking at it from purely a transgression/punishment lens.
As you said it's very complex and we can't fathom the cheshbonos. But that doesn't mean that we can't realize (I am intentionally not using the word understand) one (or possibly multiple) causes while still accepting that we don't realize the other causes.
In addition, I would just mention the inyan of things that happen to klal yisrael in general, and the fact that at the same time it is happening to each individual at the same time, and there is of course a cheshbon for both. My understanding is that Rabbi Miller is discussing the generality, but not the specific occurrences to the individuals.
As I tried to answer this, I went back to the article in Boruch999 's original post to try to re-read the quote.
"We're too much involved in gentile ideas" - what does that mean exactly? To me it means that were too integrated with gentile society. We work at their companies, get involved in their government, and involve ourselves in their communities.
To me it means that hashem is causing anti-semitism on college campuses because frum jews shouldn't be there. Or that because the Jews in Jersey City should have found a way to stay in williamsburg. Or, that because of Jews like me who live in less-frum areas, who are among the few frum jews in their companies, who navigate letting their kids play in little league without letting them play on shabbos are causing pain and suffering to other jews, because we all need a wake up call.
For my entire life, I've always been raised that the opposite was true. There are always goyim who will hate us because we are jews. There will always be other jews that hate us because of our level of observance. But if we act above board, and we teach them about our beliefs, they will have more respect for us and will understand us better. It's not a lowering of standards, but extending the richness of yiddishkeit to the world.
If I misinterpreted what is being said, please enlighten me?
(Also, R' Miller passed away over 20 years ago. The article posted quoted a speech from 1986 - clearly that speech wasn't talking about today's anti-semitism, and I wonder what the original context was?)
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