Historically we have not been at all kind to our fellow human beings. Just in recent history I can think of African slavery, the Civil Rights Movement, the slaughterings in Darfur, the Civil War, the Japanese slaughters in China during WW2, the Holocaust, Stalin's Purges, and countless cases of rape, torture, and abuse (against adults and children). Even when we're not causing the death of the innocent, or even, to a certain extent, killing those who are not innocent in a manner that is unnecessary, there are plenty of instances where we are incapable of treating each other with at least a marginal level of equality. Discrimination is rampant, controlled by faulty, corrupt governments or supported by religious doctrine. Who can and cannot have something has in the past been determined by skin color or recently by sexual orientation. Being different is simply unacceptable in human society.
And what about the animals? Animals have it worse than humans do, for the most part. Many of them are kept in cramped pens and slaughtered without the benefit of painless dead--often times they are slaughtered in a brutal way, without compassion or care that they too can feel pain and fear. Rats, mice, rabbits, other rodents, and even members of the Great Ape family, of which we are a part of, are subjected to medical testing, serving to provide us the apparatus needed to produce the appropriate medicines for what ails us as human beings (something of note to mention here is that much of this same research on the medical end has helped us to help animals as well, though the animals in question might not care about that at all). Zoos across the country frequently put animals in enclosures too small and inappropriate for a particular species. If that isn't a concern, then the idea that animals are kept in cages for our entertainment, while systematically being destroyed by human encroachment on their habitat, or excessive human hunting, should be.
What does this say about how we will treat alien lifeforms? Let's be realistic about this, for lack of a more efficient way to see things. It is, in theory, inevitable that we will find alien life. Such life will probably have similarities to us in the same way that animals have similarities. Whether we find intelligent life is entirely up to speculation, but I do believe we will encounter conscious life, if not in my lifetime, then in the next two to three hundred years. That sounds like a long time, but we have to consider now, while we are still capable of seeing the future, what to do if and when we meet these alien creatures. People will be clambering to do medical testing, to string them up on the wall for examination, to stick them in cages for the amusement of the masses. Anyone who suggests this isn't something we are capable of doing is blind to the reality of how we really are as human beings. But it doesn't have to be this way. We don't have to ignore what is a probability in the future by refusing to discuss the possibility. By the time human beings determined that we were treating animals wrongly it was already too late. We can't bring that same fate to creatures of other worlds, especially if such creatures are not as technologically advanced as we are.
In Star Trek they have a prime directive, a rule that attempts to govern the manner in which Federation ships deal with new civilizations and new intelligent species (and probably lesser-intelligent beings as well). As silly and ridiculous as such a thing might sound, we need a prime directive of our own. Barring disaster, we will be moving into the stars to seek out new planets, new homes to send our bloating population. We have an obligation as a race of beings who will be capable of interstellar flight (something I am absolutely certain will happen provided we don't blow each other to smithereens) to consider our impact on other worlds. Yes, we have to pay attention to the probes we send out. They have to be sterilized to prevent accidental infection of alien ecosystems with Earth-based bacterium and viruses. But we also have to pay attention to ourselves. We have to imagine how we would feel if a superior alien species came to Earth and subjected us to medical testing, to psychological torture and unintentional, or intentional, infection by alien agents (though many would argue that such a species is already visiting us). We no more want that than any alien species we encounter does.
Some might ask why any of this matters. Why should we care about species we don't know exist, or for that matter, aren't human? Such questions are still asked now of particular racial groups. The reason it matters is the reason anything matters in life. We have every right to exist, just as any animal does. Likewise, any alien creatures we encounter have the same right to exist on their own terms, not ours. Because something isn't human doesn't mean that we can't treat it with the same respect we give ourselves in modern times. Clarification, of course, must be given here. I do not mean how we have treated our fellow humans in the past, or necessarily in the present, but in how we are supposed to treat one another: with some level of respect. Never mind that there are people who ignore this general humanistic ideal. Even where we disagree, there is respect (to a certain extent, and I won't argue that such respect does break down; we are a violent and often brutally anti-empathic).
Alien beings must be protected from us just as we need to be protected from ourselves. The inevitable outcome of human laxness will produce more problems than humanity can deal with. We have a hard enough time addressing the human/animal issues in existence on Earth, let alone attempting to deal with human/alien/animal issues in systems many lightyears, perhaps even hundreds of lightyears from home. At that distance communications break down and become nearly useless for anything beyond sending update reports. Ten, twenty, maybe one hundred years between messages means that our human agents are living the colonial life, governed by an Earth that simply can't provide the infrastructural support necessary for a stable colonization effort; they are essentially on their own. We have to have codes, rules, laws, prime directives, etc., to govern ourselves on these faraway journeys. The sooner we realize all this, the sooner we can faithfully address the problem of human interaction with non-human creatures, the better we'll be able to deal with the future.