Against Blissey, another common Latias counter, Latias has to predict perfectly and use Trick. And even after Trick, Blissey can still force Latias out with Seismic Toss or Ice Beam. Trick is a one-time use for Latias, which means that Latias only gets one chance to remove a counter with Trick. Teams often carry more than one Latias counter, so even if Blissey gets Tricked, ones team will probably be able to deal with the less-threatening Leftovers Latias. Latias has many viable counters and checks, making it not be Uber.
To add to this, many teams are using Choicers to absorb Trick. There's Scarf Flygon, Jirachi, Tyranitar (obviously), Heatran, Metagross, Manaphy, Rotom-A, Togekiss (I've actually seen a few), Gengar, Infernape, Magnezone, Specs Jolteon, and Band Scizor. These pokemon commonly run Choice items as their main set (besides Togekiss & Manaphy, but are very good Scarfers). They're all quite popular in the suspect metagame, and frankly, if Blissey is run along with one of these pokemon, Latias is going to be putting itself in quite a bit of danger if it tries to Trick. Blissey + Choicer is quite a good combination for taking down Latias, because if Latias makes even one wrong move it'll either be crippled, severely injured, or dead.
Another set I've been seeing to check/counter Latias is Specially Defensive Skarmory (though I really really hate this pokemon). This thing is quite evil, because it can actually use Latias as setup bait to lay down Spikes. It may be hard for Latias to come back in after because Skarmory will be busy Whirlwinding the hell out of the opponent's team, and Roosting off the damage. Seriously, if you're underestimating this thing because it has lower raw base stats for Specially Defending, you're in for some trouble, because it more than compensates for it with its resistances, and essentially have no big 'physical weaknesses' despite no EV investment in Defense. A Specs Surf from Latias actually only does 37.1% - 44%, which isn't hard for Latias to Roost off. The only thing Skarmory needs to watch out for is Thunderbolt or HP Fire, which I've been seeing very little of.