Protagonists are always human, or at the very least humanoid (the "rubber-forehead" alien). This seems particularly true in sci-fi works, where humans and near-humans embody the majority of the known races and/or are the race we spend the most focus on. In fantasy it's a little less the case. Elves, dwarves, and other races have stepped in more often as central characters, but again those are near-human, in some cases even more so than in fiction. Other genres, obviously, obey this rule all the closer.
People say that this trend is due to authors and readers alike being more comfortable with familiarity. We are humans, and so we write about humans and things that look like humans. Admittedly, the bipedal form is very good at what it does. It has just enough legs to stand upright and get around quickly, without having so many it trips over them. It has enough arms to perform tasks of reasonable complexity, utilizing one as the primary manipulator, and the other as a complement to support the shortcomings of the first. Two is a company, three is a crowd, as I believe the saying goes.
Some authors make their characters animals, but even those tend to preserve the basics of bipedal life. Paws and fins can be used like hands, because again hands are really good at what they do. Applying fine motor control to whatever's in front of you, backed by sufficient intellect, is a solid path to cool innovations like splitting atoms and space travel.
I ask the masses to share their opinions on how the bipedal method could be fundamentally changed, while still preserving the potential for, say, standing amongst the stars one day. Perhaps a race evolves to manipulate its surroundings through tones of projected sound, and that, wherever it takes place, is enough. Perhaps a supremely complex ecosystem of plantlife, like in the movie Avatar, decides it needs to head elsewhere and intentionally cracks its planet apart, flying elsewhere in the galaxy on the pieces. To any who have read the work of Douglas Adams, remember the Hooloovoo: hyper-intelligent shades of the color blue. How would those even work? Would a new coat of paint be like an apartment complex to them? Would they communicate through flashes of light? They might not even need to develop space travel, being able to simply hitch a ride on blue-shifted starlight.
I think some authors have trouble realizing the full potential that comes with writing. It is the creation of an entirely new world, one that need not be subject to familiar laws. So long as it has some kind of structure to it, and the reader can make enough sense of that structure to spend time following the plot as opposed to unraveling the insanity, everything is golden.