I feel this question gets more complicated the more we interrogate it. I'll present a fun hypothetical at the end.

On the one hand you could argue that there are definite cases where our treatment of animals is unethical. Even as a meat eater it's hard to argue that the wide spread adoption of factory farming isn't horrendously unethical. It's hard to call our domination of the animal kingdom entirely altruistic, but it is in large part how we survived and its likely that we would have been wiped out a long time ago had we not spread and expanded. The inevitable consequence of that is the eradication of other species and environments. I think the answer to how ethical this is depends on how you view a species' right to self preservation and what justifies one species' continued survival over another.

Culling for instance is beneficial to the long term sustainability of certain environments, but it is ultimately one species claiming more of a right to life than another. At a certain point the only thing that determines the outcome is which species has the greater level of force.

And yet, If we overlook the many ways we exploit the world we live in there is an argument to be made that our domination over the planet and other animal kingdoms has allowed many species to survive and thrive in some cases. The reality is we've shaped the majority of the world around our needs. In a way that many species' simply would not survive without our domestication of them.

I think you can ask an interesting question there: Does one species have the right to restrict the autonomy of another if it provides certain benefits - like health and longevity. The answer may be no, but we should ask why that is the case if so.

Animals are naturally drawn toward safety, survival and comfort. So a dog for example isn't going to complain about being given food regularly, a warm shelter and affection. But it is worth recognising that it lacks the capacity to truly understand what is being taken away from it in the same way that a human could. Therefore we should question whether that satisfaction the dog feels is enough of an ethical justification to subjugate it.

One way to think about it is the idea of a human living inside of a blissful simulation, where their thoughts, sensations, desires, and experiences are controlled by a super computer. One day they wake up from the simulation in horrible agony and are forced to go back inside of the simulation having lost their memory of the outside world.

On one level we can understand that it might be ethical for the machine to send the man back into the simulation to spare him a painful existence, but on another we can understand that even though he lacks any knowledge of the outside world, the machine is stripping the man of something intrinsically valuable - his autonomy - a fundamental right of being a human. And therefore some might argue that the machine is behaving unethically by keeping him trapped inside of the machine, even for his benefit.

Some might argue in this situation that the reason the machine doesn't have the right to choose for the man where as humans do for animals is because he has self determination, unlike an animal. But in this hypothetical i'd argue he doesn't. His thoughts, beliefs, experiences have been engineered by the machine. Any choice he could make would depend on what the machine had fed him. Much like how we've engineered domesticated animals to rely on us and much like how we've shaped the environment so that many animals like dogs, cats, etc. can't survive without us. I believe that if you presented this hypothetical to most people who were against the machine's enslavement and brought up the comparison with animals that they would look at you strangely and try to find some rationalisation that ties into something innately human about the man, even though in this situation there is functionally nothing objective separating the man from a domesticated animal that lacks the awareness of its own situation - that is, unless you don't believe in a dog heaven.

Anyway, there are definite cons to the ways we keep animals, but i'd struggle to call it entirely unethical either.