Even if it did cost $1000, which it doesn't. Tax pays the salaries and materials to do the research, which is more like 10k to 100k, an additional 1k overhead is a drop in the ocean.
It's actually more than $1000. PLOS ONE starts at $1350 and tops out over $2000.
And for a lab that's publishing a lot, it can add up. Some labs are putting out 10+ pubs a year. And depending on the field, that $10-20k can be a big deal.
FTA:
>But that financial model requires authors to pay a processing charge that can run anywhere from $1,500 to $3,000 per article so the publisher can recoup its costs.