Be careful with those blanket statements. People that have some of those older Bonanza's that they fly interspersed with other aircraft might disagree with how easy it is to "train away" those bad habits. It makes it tough when one airplane has the flaps/gear levers reverse positions from the other. When I first started flying a 1970 V35B is when I quit reaching for the flap handle on roll-out.
To chime in on the larger picture I'll just say that in my opinion there may be times/situations where retracting flaps during landing is an acceptable, nay necessary procedure. That said, I'd much rather see it taught as one of those tools you keep in the tool box for when it's needed, rather than teach it as a 'normal' procedure. For sure when you get to larger/faster aircraft that particular tool is going to be taken away from the pilot and I think it's better to not have it as an ingrained habit at that point.
Teach how it can be used in specific circumstances - OK. Use it when you need to - OK. Making it a habit if it isn't truly needed - not so OK.
YMMV.