Rubio said he supports the 2001 decision by then-governor and now-opponent Jeb Bush to move the flag from the capitol to a museum in Florida.
But as a state House member in 2001, Rubio was one of the sponsors of a measure to prohibit the "relocation, removal, disturbance, or alteration of a monument, memorial, plaque, marker, or historic flag commemorating or memorializing specified wars and military engagements," including the Civil War, "permanently displayed on public property of the state or any of its political subdivisions."
Rubio spokesman Alex Conant told the Huffington Post that Rubio, "along with four other Cuban-Americans, two African-Americans, and a Jewish Democrat co-sponsored this legislation” to protect "war monuments."
In his most expansive remarks on the deadly mass shooting at a black church in Charleston that has sparked a national debate over the flag, Rubio said the white man charged with the killings "carried out an act motivated by racial hatred."
"It's an atrocity. It's a horrifying instance," said Rubio.
He said the suspect "is full of hate in his heart."