How long after physical therapy is your shoulder supposed to hurt?

Varies. Sometime therapy makes the shoulder feel better. Its not uncommon to be in some pain after therapy. It can help if you ice down after the session. Taking nsaids like Ibuprofen if approved by your doctor can also help minimize the pain after therapy.
Not long. Depending on the shoulder condition and the type of physical therapy you had, the duration of pain will vary, but purely physical therapy related pain is normally short lived (1-2 days in most cases). Also, the type of pain is usually not much worse than the pain present before physical therapy. If significantly worse, you may need to seek medical attention.