When I decided to get back into shooting after 15 years [moved/college/life/etc], I researched and bought a .40 as my first handgun. S&W 410 was what I could afford.
I developed a flinch that took me 5 years to remove. Of course I hit the range about once every 3 months during that time, but it lasted a LONG time.
I sold the handgun within 2 years of buying it and went to 9mm/.45acp and .357mag/.38special. Those are the guns that I used and liked.
Based on my experiences, I'd say the shooting instructor's observations make sense. Those are my experiences over the past 10 years also. My personal experience is that the .40 is my least favorite common semi-auto round. I'd pick .45 or 9 above the .40 for pleasure at the range any day.
That said, I've recently picked up a couple of .40s and my flinch with it is almost completely gone. I still don't enjoy the recoil as much as either 9mm or .45acp.
Heck, I would rather shoot 50 rounds of .44mag through my SRH [loaded to around 900 ft/lbs of ME] than 50 rounds of .40 [normal 400 ft/lb ME rounds]through my G22 or BHP.
But, that may be a rationalization to use my SRH more often!