Looking into what exactly the Marshals are I found that their job included the subdivision of the Office of Protection Operations, which would include the protection of high-end government officials including the Supreme Court. So why wasn't it decided for them to protect the PODUS?
While the US Marshals had held the responsibility for protecting federal judges since their inception in 1789, they were never seriously considered for the role of Presidential protection for a number of reasons. The US Marshals were distributed, and while they enforced the decisions of their district judge, they enjoyed a lot of autonomy. There was no executive presence for the Marshals in DC until the mid 1950s, with the US Marshals Service being created in 1969 to support the Marshals in the field.
The Secret Service was a centralized organization with an executive office in DC reporting to the Secretary of the Treasury, were really the only federal law enforcement agency with experience in investigations, and for decades had been exceeding their mandate by providing protective services to the President and his family. The only real debate in Congress was whether this responsibility should fall to the Secret Service or the Secretary of War and the US Army.
Secret Service Chief, William P. Hazen, made the unilateral decision to provide two agents for the protection of president Grover Cleveland after the assassination of James Garfield followed by two agents in Colorado apparently learning of anarchists or cranks who were threatening to assassinate Cleveland. He would also provide three agents to protect Cleveland's family in Buzzard's Bay, MA when Mrs. Cleveland called Hazen after being told by local police of an alleged plot to kidnap the family. Both actions were taken by Hazen without the knowledge of the Treasury Dept. or Congress. They continued to provide protection to William McKinley and his family, but these actions would come back to bite Hazen in 1898 when it was discovered by the Treasury. Congress was furious, and protection of the family especially infuriated detractors as it reeked of royalism.
Hazen would be demoted and replaced as Chief by John E. Wilkie. Ironically a few months later Congress would mandate that the Secret Service provide Presidential protective services for a limited duration when war broke out with Spain, with four agents paid out of an emergency war fund.
It was the assassination of William McKinley that led Congress to finally consider providing some sort of more permanent protection for the President. Congressmen who preferred that protection be the responsibility of the US Army pointed out that there were three Secret Service agents present when McKinley was assassinated in 1901 at the Pan American Exposition in Buffalo, NY. But there was even stronger opposition to the use of US Army soldiers as some sort of "Presidential Guard" which many thought smacked of monarchy.
Despite all the debate, the idea of presidential protection was never voted on and Wilkie continued to provide protection to Theodore Roosevelt and his predecessor without a mandate and to the objection of absolutely no one (other than perhaps Roosevelt.) Presidential protection finally became authorized by Congress through the introduction of a single line in the Sundry Civil Expenses Act of 1907. The use of Secret Service for presidential protection was an issue in the election, but not as much as the use of Secret Service agents to investigate false homestead claims, which led to the creation of the predecessor of the FBI.
The role of presidential protection was further strengthened in 1930 when the DC and park police guarding the White House were placed under the control of the Secret Service by Herbert Hoover who was angry that they had allowed a tourist to waltz past the guards and intrude on the Hoovers during dinner.
There were a number of assassination attempts on Presidents and candidates including Theodore and Franklin Roosevelt, but it was the attack by Puerto Rican nationalists on Truman in the Blair House, killing White House policeman Leslie Coffelt and leading to Congress making presidential protection a permanent duty of the Secret Service.