They can go to their own Houses, and do not have all of their classes together. The canon books, and MoR, spend considerable time focusing on inter-house interaction because that's where the interest lies, but a Hufflepuff who wanted to avoid bullies of other houses could likely do so at least 90% of the time.
And as well as the reduction of social abuse via the reduced time spent with jackasses it can be a whole lot easier to tolerate social aggression if it comes from outside what you identify as the most local social hierarchy. If a Hufflepuff is insulted by Draco it may be a minor nuisance but if it was a high status Hufflepuff like Neville bullying them it would probably seriously damage their mental health over time.
Update: This post has also been superseded - new comments belong in the latest thread.
The second thread has now also exceeded 500 comments, so after 42 chapters of MoR it's time for a new thread.
From the first thread: