“He should refuse to be swayed by frenzied passion or surface patriotism, but should remember that the truest patriotism is shown only by loyalty to one's highest moral convictions.”

Statement in the House of Commons (24 July 1990) http://www.margaretthatcher.org/speeches/displaydocument.asp?docid=108162
Third term as Prime Minister

Explaining his veto http://www.freedomforum.org/templates/document.asp?documentID=16297 of a bill [HF 2598*/SF 2411/CH 391] requiring public school students to recite the Pledge of Allegiance at least once a week (22 May 2002)
Context: I believe patriotism comes from the heart. Patriotism is voluntary. It is a feeling of loyalty and allegiance that is the result of knowledge and belief. A patriot shows their patriotism through their actions, by their choice.
Chapter 391 is not about choice. In Chapter 391, the State mandates patriotic actions and displays. Our government should not dictate actions. The United States of America exists because people wanted to be free to choose. All of us should have free choice when it comes to patriotic displays... a government wisely acting within its bounds will earn loyalty and respect from its citizens. A government dare not demand the same.
There is much more to being a patriot and a citizen than reciting the pledge or raising a flag. Patriots serve. Patriots vote. Patriots attend meetings in their community. Patriots pay attention to the actions of government and speak out when needed. Patriots teach their children about our history, our precious democracy and about citizenship. Being an active, engaged citizen means being a patriotic American every day. No law will make a citizen a patriot.

Behaving on a still higher moral level were the astronauts who went to the Moon, for their actions tend toward the survival of the entire race of mankind. The door they opened leads to the hope that H. sapiens will survive indefinitely long, even longer than this solid planet on which we stand tonight. As a direct result of what they did, it is now possible that the human race will never die.
Many short-sighted fools think that going to the Moon was just a stunt. But the astronauts knew the meaning of what they were doing, as is shown by Neil Armstrong's first words in stepping down onto the soil of Luna: "One small step for a man, one giant leap for mankind."
The Pragmatics of Patriotism (1973)

Various; earliest source The Use of Force in International Affairs http://www.worldcat.org/oclc/21414360 (Philadelphia: Friends Peace Committee, 1961), 6, and popularized by various users in the 1960s:
If what your country is doing seems to you practically and morally wrong, is dissent the highest form of patriotism?
Dissent is the highest form of patriotism http://wiki.monticello.org/mediawiki/index.php/Dissent_is_the_highest_form_of_patriotism_(Quotation), Thomas Jefferson Encyclopedia
Other form by historian Howard Zinn Dissent In Pursuit Of Equality, Life, Liberty And Happiness: An Interview With Historian Howard Zinn http://www.tompaine.com/Archive/scontent/5908.html by Sharon Basco, TomPaine.com http://TomPaine.com, July 03 2002 (The quote can be found in the first sentence of Mr. Zinn's first answer; nowhere in that article does Howard Zinn attribute that quote to Jefferson.):
While some people think that dissent is unpatriotic, I would argue that dissent is the highest form of patriotism.
Law professor Jim Lindgren of The Volokh Conspiracy has traced the possible origin of this saying back as far as the 11 November 1984 obituary of pacifist activist Dorothy Hewitt Hutchinson in the Philadelphia Inquirer, quoting a 1965 interview. The direct quote there is: "Dissent from public policy can be the highest form of patriotism," she said in an interview in 1965. "I don't think democracy can survive without it, even though you may be crucified by it at times." According to the professor's research http://volokh.com/posts/1146554363.shtml, the misattribution was popularized in the 1990's by ACLU president Nadine Strossen. Bill Mullins of the American Dialect Society did further research http://listserv.linguistlist.org/cgi-bin/wa?A2=ind0605A&L=ADS-L&P=R1297&I=-3.
Misattributed

The Lion and the Unicorn (1941), Part I: England Your England
"The Lion and the Unicorn" (1941)
Context: One cannot see the modern world as it is unless one recognizes the overwhelming strength of patriotism, national loyalty. In certain circumstances it can break down, at certain levels of civilization it does not exist, but as a positive force there is nothing to set beside it. Christianity and international Socialism are as weak as straw in comparison with it. Hitler and Mussolini rose to power in their own countries very largely because they could grasp this fact and their opponents could not.

Source: Leftism Revisited (1990), p. 327

Explaining his veto http://www.freedomforum.org/templates/document.asp?documentID=16297 of a bill [HF 2598*/SF 2411/CH 391] requiring public school students to recite the Pledge of Allegiance at least once a week (22 May 2002)
Context: I believe patriotism comes from the heart. Patriotism is voluntary. It is a feeling of loyalty and allegiance that is the result of knowledge and belief. A patriot shows their patriotism through their actions, by their choice.
Chapter 391 is not about choice. In Chapter 391, the State mandates patriotic actions and displays. Our government should not dictate actions. The United States of America exists because people wanted to be free to choose. All of us should have free choice when it comes to patriotic displays... a government wisely acting within its bounds will earn loyalty and respect from its citizens. A government dare not demand the same.
There is much more to being a patriot and a citizen than reciting the pledge or raising a flag. Patriots serve. Patriots vote. Patriots attend meetings in their community. Patriots pay attention to the actions of government and speak out when needed. Patriots teach their children about our history, our precious democracy and about citizenship. Being an active, engaged citizen means being a patriotic American every day. No law will make a citizen a patriot.

Letter to James Warren (24 October 1780) http://www.gutenberg.org/etext/2094