Again, that's true and it counts to the advices the Gods gave him against fraternizing with Zeno. But from everything Goku actually SAW of Zeno is a child who's been nothing but friendly to him, merciful of his disobeying underlings and helpful on defeating his unstoppable enemy. It's arrogant of Goku to think he knows better, especially since those guys warning him did nothing but put up with his shit, but from his point of view, there's no way he could think Zeno would murder everybody. Remember another trait of his is seeing the best in everybody. It's a mistake, but it's treated as such. And we haven't seen his reaction to the Universe destruction rule, so who knows what he'll think. If we go by his character up to now, he will take responsabillity eventually, much like he did in the Android arc or the Buu arc (of course, with Super you never know). He did this stuff before, it's nothing new. It's the way he is. The fact it is getting some attention is good, since before now no one called him out on it in-universe. Krillin went with sparring Vegeta, everybody went with not killing Gero, his putting Earth and eventually the Universe in the Buu arc got hand-waved at the end. Now Beerus is actually scolding him for being naive.
It should be also noted that without trying Goku did something that no one, not Beerus or Whis has done. He made friends with Zen'o and even gave him a playmate. So already Goku has an experience with Zen'o that isn't matched with Beerus and Whis. The same thing happened with Beerus when all the Kais were shocked that Goku was able to win over the God of Destruction, who was considered a force of nature just like Zen'o.
So from Goku's POV, Zen' was no different than Beerus. He was told he was destructive, petty, unpredictable, and shouldn't be mess with. Yet, from Goku acting recklessly, he gained two powerful allies. So why would Goku assumed Zen'o would be any different, especially since he comes off as far nicer than Beerus even now? We, as the audience, know that Beerus is right because we have been told what the stakes are going to be. So for us, it's easy to that things will go wrong. If we went in blind like with Zamasu, was Goku or Beerus more right about him, we may side with Beerus more, but we wouldn't dismissed Goku's view that maybe Zamasu isn't as bad as he seems.