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"...Previous discussion on Free Republic would seem to indicate that the Creationists believe that a letter of recommendation is an entitlement. They also claimed that such letters could not be refused on the basis of civil rights..."

Rather it would seem that bigotry backed by "science" is acceptable.

That is not how I read the article. The instructor was asking the student to give the scientific explanation for the existance of the current forms of life that inhabit the Earth. Belief was not brought into question, only whether the students could demonstrate that they properly understood the subject as taught. Let me give you an identical counter example, with a less inflammatory subject:

A Professor of Political Science asks his students the following question:
"What is the basis of legitimate authority for Communist Governments?"
If a student's reply was, "There is none, I don't believe in the Communist form of government, and I won't answer this question." then the instructor would have every right to say that the student was non-responsive, and failed to demonstrate that they had absorbed the material of the Political Science class. (BTW, it makes no difference if the question was about Communisim, Socialism, Anarchy, etc. Each form of government makes a claim as to it's legitimacy, and the student should understand and be able to recite each).

So, personal BELIEF is not the point. Can you RECITE and EXPLAIN (and therefore demonstrate UNDERSTANDING) of the material you are expected to learn in the subject.

--The instructor was asking the student to give the scientific explanation for the existance of the current forms of life that inhabit the Earth. Belief was not brought into question, only whether the students could demonstrate that they properly understood the subject as taught.--

Actually, that is not correct. The question was:

"How do you think the human species originated?"

And he required a "rooted in science" answer. If you gave the wrong "opinion" you didn't get the letter.