One of the historical reasons nobody pays much attention to the lower leagues is because we don't have promotion/relegation here. So if you follow an MLS team you'll never see them in the lower league as we don't have relegation, and if you're a fan of a lower league team they can't get promoted to the top league. Which means there's zero connection between the leagues, and not much incentive for MLS teams to play in the tournament as things currently stand. Only a very few USL teams have ever been "promoted" to MLS, but to do that they have had build new stadiums <and> pony up $200 million or so to join the league as an expansion team. So if you're running a USL team that's been a successful business there's almost a disincentive to move up to MLS because of the huge cost of entry (as opposed to England, say, where "all" you have to do is be in the top three of the next lower league to get promoted).I haven't been a fan of soccer in the US long enough to understand the historic significance of USOC, but at this point in time the only reason I can see for MLS teams to participate would be to give lower league teams the chance to shine against Messi and co, so to speak, to make the pyramid more robust and viable. But if MLS fans are tuning USOC out anyway, that's also not working. MLS getting out of USOC is pretty much an acknowledgment of the gulf that exists between MLS and any viable lower league.
So the bottom line is that from an MLS perspective the US Open Cup has little benefit and potentially clogs up the schedule. And because of the disjointed soccer landscape here there's not much incentive for the upper leagues to play against the lower leagues. So basically there's no real soccer pyramid here, more like there's several unconnected cubes that have little to do with each other.