Space can be a dangerous place for humans—seriously, we were not made for a cold, radiation-filled vacuum—and technology is the only thing that can keep humanity safe while traveling it. No tech, no space travel for you. Mother represents that technology.
Mother in the Machine
"Mother" is the ultra-creepy name given to the Nostromo's computer mainframe. She, erm, it provides the crew instructions from the Company, and keeps the crew safe by regulating the systems of the ship, a necessary component of the not-dying part of space travel.
Its name is meant to evoke connotations of safety and comfort. Like a baby, the crew is coddled and nurtured by her, protected from the harsh world outside. Without it, they're essentially a bunch of space babies unable to survive on their own.
The coddling, nurturing element of Mother is further emphasized by the room the crew uses to interface with it. The brightly lit room contrasts with the darkness of the planet and the parts of the ship where the crew interacts with the alien; it's shaped like an egg, imagery suggesting a safe womb. Unlike the alien's organic, fleshy egg, Mother provides a high-tech womb that pits the safety of technology against the dangers of nature.
And just like children, the crew places their trust in Mother—uncritical, wholly accepting. Big mistake. Huge.
Dallas, for example, is totally complacent when it comes to Mother. When explaining to the crew why Mother changed course, he says, "She's programmed to do that should certain conditions arise. They have" (Alien). He doesn't question the situation; he just goes along with it, like a kid buckled into the backseat while his mom takes a quick detour. After all, a computer programmed to protect can't lie or conspire, right?
Of course, Dallas's complacency becomes wickedly ironic when it turns out that the Company has programmed Mother to help them retrieve the alien. See, Mother might take care of the crew, but she certainly doesn't care about them. She—it—is unfeeling and impersonal, nothing more than electric charges passing through silicon. It's not actually a mother but a tool. And, like any tool from the first crudely hammered stone to the flashiest animated PowerPoint, it's only as good as its user.
After all, Mother is no HAL 9000 actively trying to harm the crew of the Nostromo—but she can be used for that purpose, as when Ash uses Mother to retrieve and work toward his secret mission. But she can also be used for good, as when Ripley uses Mother to discover said secret mission and ultimately save the remaining crew. As she tells Ash, "I've got access to Mother now, and I'll get my own answers, thank you" (Alien).
Throughout the whole bloody massacre, Mother goes about her tasks with cold, impersonal calculations. We see this ultimate coldness at the end of the film, when Mother is unable to shut down the self-destruct system even though it means killing the crew. The commands have been inputted, and she must follow through.
Ultimately, Mother and the alien might have more in common than it might seem. Although one represents technology and the other nature, they both act in whatever way their programming tells them to. The only difference is that the alien is programmed by nature and its genes, whereas Mother is programmed by a programmer and code.