It's not the store manager that annoys me - we've had one who had his retard setting set to 11, but apart from that we've been quite lucky. No, the people that dissuade me from the FLGS are the other people. I should learn to stay out of arguments, but I can't help it sometimes and I get caught into an argument with a whole group of elitist ubergeeks who play Guard with Conscripts, Deathwing, and Footdar and will NOT admit that they are a bad army.
The problem that you can easilly run into in this case is when the skilled player comes along with one of these higher caliber armies, as like facing a skilled marksman with a more accurate rifle, you'll have to work hard to win, and will be punished harder for your mistakes. Does it make you less capable of winning? Only marginally, as even a simple army can have devastating effects in the right hands.
Just to finish up on my poor analogy here's an article about a Finish sniper who fought in the Winter War against Russia. Using just a rifle (a rather short varient of the Mosin Nagant) with just the iron sights and his skills he racked up 505 confirmed kills against the Russian Army. To me it's proof that a skilled man with a weapon he's comfortable with (he chose the rifle because it fit his small size) can do great things despite the odds. And less lethally so can a wargamer.