The Supreme Court was hostile to many New Deal programs because it was made up largely of justices who had been appointed by conservative presidents. This meant that they largely shared the common conservative attitude towards government regulations of the time. They felt that the federal government should not be able to impose many, if any, regulations on business.
The Court used a variety of legal justifications to strike down regulations. It found, for example, that a chicken processing plant in New York City was not part of interstate commerce because the chickens were not going to be shipped to other states after they had been slaughtered. But the specific legal rulings are not what is most important. Basically, the Court struck the laws down because it felt that government regulation was an infringement on people’s economic freedoms.