In a statement released hours before the game, Trump honored the troops and said he and Melania will "thank them for our freedom as we proudly stand for the National Anthem."
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"We owe these heroes the greatest respect for defending our liberty and our American way of life. Their sacrifice is stitched into each star and every stripe of our Star-Spangled Banner," Trump said.
The statement comes at the conclusion of a contentious NFL season where Trump himself got personally involved as an increasing number of NFL players kneeled during the national anthem in an effort to shed light on social justice issues.
"Can you believe that the disrespect for our Country, our Flag, our Anthem continues without penalty to the players. The Commissioner has lost control of the hemorrhaging league. Players are the boss!" Trump tweeted on Nov. 24, one of the many times he sounded off on the issue.
Proponents of the protests say they bring attention to social issues impacting minority communities, while Trump and other opponents find the displays disrespectful to the flag and members of the military.
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In response to the scrutiny, the league met with players, owners and other stakeholders last year and later announced that it would donate $90 million to support social justice causes promoted by the players. The league recently launched Let's Listen Together, which focuses on police relations, criminal justice reform, education and economic advancement, according to its website.
Full text of President Trump's statement as released by Press Secretary Sarah Sanders:
"As many Americans come together to watch the Super Bowl, Melania and I extend our greetings and appreciation for those who make occasions like this possible, particularly the brave men and women of our Armed Forces.
"Though many of our Nation's service members are unable to be home with family and friends to enjoy this evening's American tradition, they are always in our thoughts and prayers. We owe these heroes the greatest respect for defending our liberty and our American way of life. Their sacrifice is stitched into each star and every stripe of our Star-Spangled Banner. We hold them in our hearts and thank them for our freedom as we proudly stand for the National Anthem.
"We send our best wishes for an enjoyable Super Bowl Sunday. May God bless and protect our troops, and may He continue to bless the United States of America."