Another reason for Rafa to reject Atletico Madrid is due to the fact that he is deeply related to Real Madrid, having developed as a junior player in their academy, then coached their youth and reserve team(Castilla) and then been the assistant manager of the their first team. As he himself admitted, he harbours the ambition to coach Real Madrid one day although he rejected them twice while he was manager of Liverpool. Accepting their offer would surely have killed any chance of coaching Real Madrid since the 2 clubs are fierce rivals.
However, the most likely reason for Rafael Benitez to reject Atletico is probably due to the fact that he sees his future in England. He has more control over the team affairs and he is a manager who likes to build on the long term, while pushing the club to win trophies in the short term. In England, he is a manager while overseas, he would be just a coach. One thing he did say when he was Liverpool's manager is that "in England, the fans remember", probably referring to the fact that supporters in England remember their manager and the success he brought for a long time. All of Rafa Benitez's moves up to now seem to point that he indeed sees his future in England, confirming what he has said many times in the recent past.