Doesn't protein get digested by protease in the stomach/denatured by the hcl in the stomach so how can it enter the body through ingestion?

Digest then absorb: Proteins are made up of long chains of dozens or hundreds of amino acids. HCL and pepsin in the stomach & protease breaks the proteins down into individual amino acids, which can then be absorbed through the intestinal lining into our bloodstream. See http://study.com/academy/lesson/protein-digestion-and-absorption-process.html for more details.