As several other people have been saying, the metagame is still new and needs time to settle. As people face more and more of things like Therian forms, they will develop counters to them like everything else.
If you were referring to Amoongus/Breloom countering them, neither of them can take a Hurricane from Tornadus (either form, really). They are nice checks to rain, but a good rain team will have something to stop them from walling the time. I ran both Specs Tornadus and Life Orb Thundurus on the same team simply because I was going for a hyper-offense style of playing. One would severely dent, if not take out, any walls to rain, while the other cleaned up house.
Speaking of Breloom countering rain, Breloom actually does a great job on rain teams himself. Ferrothorn and Gastrodon, both huge banes to most offensive cores in the rain (hell, Gastrodon came into OU as a counter to Thundurus before he was banned), and both sand starters (Tyranitar/Hippowdon) can be beaten by Breloom, even if it's the original set and not Techniloom. Getting rid of his fire-type weakness is also pretty nice.