Roosevelt had been Assistant Secretary of the Navy just prior to the Spanish-American War. At that time Secnav was a cabinet position and the Secnav John Long was inactive so T.R. was pretty much in charge of the department. He was aware of the problem of time in Shifting Fleet units from one coast to another. After the explosion of the Battleship MAine the USS OREGON left San Francisco for Cuba, a trip of 66 days including coaling stops.
I would say he understood the value of the Panama Canal both economicaly and militarly. He just did't know when it would be needed, but it was there.