This is because at some point, Lynn decided to make Annie Nichols into a critique of people who parent via manuals instead of blindly plodding along doing the same stupid things Saint Marian did. The end result of her daring to question the time-tested wisdom of the woman that raised her is, as one could expect from someone with mother issues as complex as Lynn, CHAOS!!! The premise seems to be that if Anne would have put the books down and behaved just like Elly, her children would be well-behaved and support her in her older years like children are supposed to instead of acting as if they're autonomous individuals who can follow their own destinies.
That being said, only Elly and John are permitted to comment on how destructive and crazy the Nichols children are. Michael is not yet a tax-paying adult and since he is not yet fully human when he is forced to associate with them, he is no more permitted to object than April was to the Housening. Feeling bad about things, you see, is a privilege given adults; children not only owe their parents all the money spent on them, they also owe them instant obedience as well as a canine eagerness to do whatever insane thing Mommy and Daddy propose. Simply put, Mike was a bad kid because he isn't filled with unthinking glee when told to associate with Annie's whirling dervish Hellspawn.