During acid reflux and vomiting, is the burning sensation from pepsin or acid?
It is the acid that causes the burn  

Medicines like proton pump inhibitors (e.g. Prilosec), or H2 receptor antagonists (like Zantac) that reduce acid secretion reduce the burning sensation.  Medicines that neutralize the acid like calcium carbonate (e.g. Tums) also reduce the burn.  These medicines do nothing to the secretion of enzymes.  

ADDENDUM. @anongoodnurse wants references.  Maybe in exchange she will remove that pesky down vote.

Cimetidine won the team that developed it the Nobel prize - the first rationally (as opposed to empirically) designed drug.  It was designed to very specifically reduce stomach acid.

https://www.acs.org/content/acs/en/education/whatischemistry/landmarks/cimetidinetagamet.html


  Smith Kline &amp; French's multidisciplinary research team first looked at
  the physiological cause of acid secretion. They confirmed that a
  molecule found in the body called histamine triggers the release of
  acid when it binds to a specific receptor (now called the H2-receptor)
  in the stomach lining. Their aim was to find a molecule that
  successfully competed with histamine in combining with the receptor,
  but then blocked, rather than stimulated, acid release. Such a
  molecule was called a histamine H2-receptor antagonist and represented
  a new class of drugs.


This and the successor class of drugs (proton pump inhibitors) are very specifically designed to decrease acid secretion and do little else. 

The fact that billions of dollars worth of these drugs are sold means that persons suffering from reflux pain / stomach ulcer perceive that their pain is reduced by a decrease in acid secretion, and so are willing to pay.  


  Tagamet® was greeted with great enthusiasm by doctors and patients
  alike. Ten years after its introduction, it had achieved sales of one
  billion dollars and had become the world's number one prescription
  drug.