This brings the same problem fantasy settings always have: If beastman are so dangerous and stronger than humans but have the same intelligence level or are even more intelligent than humans how does humans still exist?
Common problem, yup. In most settings Elves are smarter, often faster or stronger, and incredibly long-lived so why would humans ever be in charge? The simple in universe answer is usually: humans breed like bunnies compared to other sapient creatures, and the second is that because they have a short life they have an unnatural drive compared to other races.
The isekai beast-human races presumably are just stronger humans. And they're treated like shit. There is practically no reason they shouldn't be in charge. The only real explanation I could think of is the first reason again: there are just a massive number more humans, they have more kids more often, and they culled the beast races in the past making their numbers dwindle. So an uprising might no go well due to sheer numbers.
But the actual reason is because the writer and readers are human, its what we know. So we have a main character complex that humans are often in charge... and let's be real beastkin are just waifu/husbando bait.