One must look at the situations Harry and Co. were putting themselves in... normal students were not getting into the type of "adventures" that the trio was.

To go through your examples:

 1. Sorting Hat - It is Harry's first experience at the school. He has no idea on how Sorting works. His greatest fear is being sent back to the Dursley's. 
 2. Midnight Duel - Harry is only in second week of school and already breaking rules by arranging to duel underage student. I don't about you, but my school expelled students who got into fights.
 3. Forbidden Forest - Objectively, a student has broken at least three separate rules, have an *illegal* creature, and has a magical item of unknown properties. Suspension is a valid concern in this instance!
 4. A Peck of Owls - Harry had "clearly broken" the International Statue of Secrecy. He had broken not a school rule, but a law. He would be expelled and not even be able to practice magic. 
 5. Transfiguration Class - There is no threat of expulsion here, only not being able learn Transfiguration. As this a highly dangerous subject this is not unreasonable. 
 6. Quidditch - Hooch was exaggerating just a bit. She did not want any unsupervised flying attempts. One student was already injured, she did not want to risk another. 
 7. Whomping Willow - Ron and Harry had stolen an unregistered magical item and most likely broken the International Statute of Secrecy. Upon appriving at school (as Snape makes clear) they crashed into the Whomping Willow and nearly destroyed it. Again, breaking laws and destroying property is really something to be concerned about!
 8. See above...
 9. Shrieking Shack - Breaking multiple school rules and AIDING AND ABETTING a known CRIMINAL! They are probably lucky Azkaban wasn't being mentioned!
 10. Sectumsempra- Harry nearly kills Draco. If Snape had not been there and recognized what had happened it is inconceivable for Harry to be tried for murder. Expulsion and Azkaban would seem likely.

**Recap** - Harry, Hermione, and Ron are in situations beyond what would be expected from "normal" students. **The threat and fear of expulsion (if not worse) in almost all cases is justified.**