Whalesquid, aka Hideauze, are considered holy by Earthlings. Why? Because they were originally created by humans to help humans adapt to space by becoming bodies for them via genetic engineering. How the Hideauze are treated makes perfect sense if you consider them people that can survive underwater.
The archive footage shows that The evolved humans were highly respected and revered for being pioneers in an endeavor that might have saved the human race. This respect must have been retained over time and evolved into worship.
Or it could just be simple pragmatism, given that whalesquid are apparently horrendously dangerous to fight.
The reverence is clearly cultural; the Gargantians aren't actually very afraid of them, so their borderline worship of whalesquid has to do with more than pragmatism.
The naming of the Hideauze instead of 'Evolvers,' as they were known on Earth, is actually quite telling. They're hideous in the eyes of the Galactic Alliance. A few generations of propaganda and linguistic shifts....
Chamber claims that a random glitch in the wormhole sent them to a completely random location, which happened to be Earth. One troper estimated this to be a 1 in 10^39, i.e. one in a trillion billion billion billion chance for that to happen. However, not only did Chamber end up on Earth, but Striker did as well, which implies that it wasn't a random chance. The Continental Union built a wormhole gate near Earth similar to the one employed by the Galactic Alliance. When the Galactic Alliance's wormhole collapsed, it's likely that both machine calibers fell through space time toward Earth because there was a preexisting 'fissure' located there where the old wormhole at Earth used to be.
The Wham Episode reveals to us that the Hideauze are actually genetically engineered Humans. This is actually lightly foreshadowed in episode 1. If you pay careful attention during the initial battle you can catch blink-and-you'll-miss-it shots of the Hideauze with disturbingly human(or at least simian)-like faces behind the mouths...◊
The series might end well for the Earth Humans, but the Galactic Alliance of Humankind is still out there somewhere. Not only are they said to be always on the lookout for habitable planets, there's also Ledo's distress signal which Chamber claimed would reach them in a few thousand years. It may take a really long time, but eventually they'll find Earth, and it's hard to imagine a happy outcome when that happens.