It's not a problem with .50 rifles, it's a problem with that rifle.
There are plenty of precision .50's that will shoot well under 1 MOA.
Considering the military standard of either <2MOA or <4MOA in the past of when the M82A1 went into service, 1-2 MOA is fine. You have to understand the reasoning behind the M82A1 being made. It was the first (or so is claimed by Barrett) man-portable .50 BMG rifle that could be taken into the battlefield and used effectively at long ranges against hardened targets. It wasn't designed for hitting prairie dogs at 1000 yards. Also at the time it was being put into service, the standard ammo for it was the standard .50 bmg machinegun ammo, which is far from being match ammo.
I am not sure where the notion came of it being a "sniper" rifle. It is used by some snipers, yes, but then again, so is the M4. That does not make the M4 a sniper rifle. It does make it a sniper's rifle when being possessed by a sniper, but that isn't the same thing.
I liked the Marine description of the M82A1. It is a SASR, or Special Application Scoped Rifle.
The recoil of the .50 BMG is pretty significant and Barrett realized that it needed to be toned down quite a bit for the rifle to be more user-friendly. So he basically used a 3 step system. First is the recoil spring that cycles the gun over a longer period of time than smaller caliber rifles and spreads that part of the energy out longer, dampening the feel of recoil. Next, the barrel is on springs. When the gun fires, like some canon, the barrel moves back into the receiver. Last was the massive muzzle brake. Now they have smaller brakes that are as effective, but at the time, that didn't seem to be the case.
I have to admit, there is something cool about being able to put rounds on target as fast as your crosshairs are on target. I can't say I have a real need to do it, but I have dumped magazines a couple of times.
So you have a semi-auto rifle that fires a very large and powerful cartridge and has a lot of moving parts to help dampen the recoil as well as non-moving parts. You can shoot one all day long and not be beat up by it. Okay, that may be stretching the point. I have put 200 rounds through mine in a given day and while I was tender the next day, I was better off than shooing 30 rounds of slugs out of my 12 ga shotgun.
The M82A1 isn't a bad rifle. It did what it was designed to do and did it very well, but what it was designed to do isn't what a lot of people are looking for in a .50 bmg rifle.