Many writers consider the Eldritch Abomination the same way the Trope Codifier, H. P. Lovecraft, did: as an unfathomable, destructive monster. Many say that the monster is to a human in the way a human is to an ant. Some even say that Humans Are Cthulhu to the ant, if not the real monsters.
What these writers forget is that not all humans bear animosity to ants. Unless the thing is invading your house/food supply, or is doing environmental damage (or, mayhaps, you're dealing with carnivorous ants), the average Joe is just as likely to regard the ant with zero ill will. Some of them even go out of their way to study, and even outright help, the ants. We have scientists who study them — even create ant farms for them to live in whilst the scientists complete their studies — and some people will work to preserve animal homes.
In a similar fashion, it isn't hard to imagine a setting in which eldritch entities will go out of their way to avoid harming humans, perhaps even give them a big hug (hopefully not the harmful kind). In fact, if humans, with all their limitations, are capable of great good, it stands to reason that supernatural powers are capable of even greater good.note
Another thing to consider is that these entities are capable of remembering that with great power comes great responsibility. Someone who can fly through space and time, destroy matter on a whim, and eat suns is also capable of great knowledge, wisdom, and even ethics.note In the same way you'd get in big legal trouble if you ran over your neighbour's dog, a demigod who wiped out an inhabited planet might get into even greater trouble — even if it did it by complete accident.
Finally, consider that the universe is a pretty big place. Anything swimming around in it has, essentially, an infinity-to-one chance of going on a collision course with Earth, especially if it has the ability to traverse the cosmos to begin with. Even if the creature is light years in diameter, it will be able to pass between individual stars and still have a wide berth. Anything that lands on our green-and-blue sphere probably has a good reason to be here.
This is not to say, of course, that these entities can't still be scary. C. S. Lewis' The Space Trilogy contains Eldritch Abominations which are benevolent, but still unbelievably powerful and terrifying. This is because we fear things that are more powerful than us, even if they're good — a little kid meeting a seven-foot marine, for the first time, will be terrified. However, given enough time spent together, the kid will grow to regard the marine as a friend. In the same vein, these entities may still scare us, at least at first, but if we were to get to know them, we'd find they're not that bad.
