Here's a real example:
In March I added a delayed popup to my blog to invite people to subscribe for future updates about user acquisition. It was on a delayed timer so that the reader has a chance to at least get part-way through the post. Also, if you closed it out once then you wouldn't see it again for something like 30 days.
Since then, it's been seen by 11,848 people, of whom 232 (1.96%) signed up.
Most blog readers come for the article, not for the blog or the company. They read the article then carry on with their lives, even if the article was very helpful or interesting to them.
Here's how I see it: I now have 232 people who are actually interested in learning about user acquisition, and gave me permission to send them more helpful posts. I wouldn't have this if I never asked them to enter their email. I realize the price to pay for this is mildly annoying the other 98%.
With that said, I'm trying to minimize that annoyance. I'm now experimenting with a less invasive prompt; a thin bar at the top of the screen, that also hides when you're scrolling down (presumably reading). If it still gets subscribers _and_ is less annoying to the others, then I'll keep it.
tl;dr - Companies know and don't care that popups are annoying, because they're effective. Some companies care a little and try to make the popups less annoying to those who wouldn't have signed up anyway.