Is it actually harder to read? Or do people just want it to have sound sentence structure just on principle?
It depends on the sentence.
* Some run-on sentences are completely fine, and even not ungrammatical. Generally it’s ok as long as there is a main clause and the others or subordinate. e.g:
If you knock first, you can go right in.
Or the structure makes sense to link them together:
George went to the store, he bought a cantaloupe, and he went to the post office.
Now in a writing class, they might or might not mark you down for that last one and want you to use semi-colons to prove that you get the point, but in that case it wouldn’t be any clearer.
* Some other run-on sentences would be completely fine, if the correct punctuation were used. In these cases, the correct punctuation is pretty much always an improvement and does make the sentence clearer, e.g.:
I love to write papers I would write one every day if I had the time.
->
I love to write papers. I would write one every day if I had the time.
* Some other run-on sentences need more work than that. People who write such are usually either in a rush (and they might know better and get annoyed to get a lecture), or have poor writing habits (in which case it might be more likely it will help (eventually) to point that out).