There are several good reasons.
The odds that your armed congregation will ever use a gun to stop a mad man approach zero. 350,000 congregations, say 3 meetings a week, 52 per year, roughly 55 million gatherings minimum per year, and, what, maybe 5 incidents (1/10,000,000) per year that might potentially have been stopped with a qualified, trained, armed person who can reliably take out a shooter without killing other innocents. So the odds of a 'good guy with a gun' taking out a bad guy are less than being struck by lightning, by a factor of at least 10
And for those of us who don't feel skeered without a gun on us at all times, an armed person changes the atmosphere for every one of those meetings for the vast majority of attendees, and for most of them they don't feel any safer (they aren't), and the change is negative, sometimes VERY negative. Lots of people have never shot and are simply very uncomfortable around firearms. Others may have very good reasons to fear them, and guns bring back horrible memories.
I'm not scared of guns or of people with guns, but I don't want to worship with the guy next to me with a Glock, and worry if he's sane, if he knows anything about using his weapon, if his child is going to grab it, take it out of mom's purse while she's singing the hymn and shoot me in the back, that the idiot is going to take it into the bathroom and leave it on the back of the toilet for some child to grab, etc.
So the increase in safety is zero, and it comes with it depending on who is attending, their life history, their comfort with firearms, some potentially huge downsides. Some will simply not attend if the congregation is armed. You can like that or agree or not, but that is just fact. About the only good thing is some people who for whatever reason feel obligated to be armed at all times for what are in most areas of the country irrational reasons will feel safer. Nearly everyone else AT BEST is ambivalent, and in just a huge number of cases, the gun will detract from the act of worship.