Fourteenth amendment? Never heard of it

The Federal Appeals Court in the Boston district made this breathtaking statement:

The [jury] instructions also erroneously appeared to equate acting based on any perceptions of a person's race or ethnic heritage with illegal discrimination.

Race or ethnic origin of a passenger may, depending on context, be relevant information in the total mix of information raising concerns that transport of a passenger 'might be' inimical to safety.

Congratulations, you've just legalized racial profiling! How'd you like a trip to Disney World?

Section 1 of the Fourteenth Amendment states:

All persons born or naturalized in the United States, and subject to the jurisdiction thereof, are citizens of the United States and of the State wherein they reside. No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws.

This was not the only issue on appeal. Why did the court go this far?