Jonathan warned David of Saul's plan because he was fond of him. He had made a covenant with David (1 Samuel 18:1–5) and recognized him as someone through whom the Lord was working. He did not know of any evil that David had done to deserve death and so he stood up for him. David was Jonathan’s brother-in-law at this point in time.1
1 And Saul spoke to Jonathan his son and to all his servants, that they should kill David. But Jonathan, Saul’s son, delighted much in David.