Does this only affect companies,

Does this only affect companies, or can individuals also infringe on patents by publishing design files?

In the US a patent holder rents a government granted monopoly. It is up to the patent holder to decide who to go after and that can indeed be an individual. However because it cost money to go after people it does not really make sense for a patent holder to go after an individual for infringement.

If a company had a patent and wanted to set some precedent for what it covers before pursuing other companies with it, they might decide to sue some individuals.

Sure, but living in the USA is all about the constant threat of being sued. No reason to lose sleep over it.

Even MakerBot have filed for a patent for an automated bed platform…