The advice against feeding honey to babies is not because of allergies, but because there is an -- admittedly small -- risk of it being contaminated. A baby's immune system isn't sufficiently mature yet, and this type of infection is potentially fatal.
So, yes, most parents are probably not going to notice anything bad about giving honey to their little ones. But as there is no particular unique benefit to eating honey, even the minor risk is worthwhile avoiding. This is the same reason, why pregnant women are advised against eating fresh cheese and raw fish. The risk is small, as evidenced by Japanese women eating sushi during pregnancy. But there still is a minor risk for an infection that could prove fatal to the unborn. Why take chances, if there are so many other alternative foods. And it is only for a couple of months anyway.
This is all very different from allergens. While allergies are not fully understood, there does appear to be some evidence that early exposure to allergens can reduce the statistical likelihood of developing allergies later in life. This must be traded off with the risk that allergic reactions can happen unexpectedly (i.e. somebody suddenly becomes allergic to something they previously didn't have problems with) and food allergies can easily be so severe that they are life threatening.
I never bought into the theory that avoiding peanuts for infants somehow helped them avoid developing allergies. So, these newer findings don't surprise me much. But I did buy into the precaution of avoiding peanuts for really young children, as a possible allergic reaction would almost certainly put them at increased risk of dying from anaphylactic shock.
The conclusion for us was: no raw fish during pregnancy, no raw honey or peanuts during the first year of life, but no additional restrictions after these times. We still carefully watch the kids, when they eat nuts, though -- just in case. And we generally encourage a diverse diet, always asking the kids to try new things.