Though the film tries to be objective, given the title of the documentary and this quote from NOVA Senior Executive Producer Paula S. Apsell, I find that highly unlikely. Apsell says:
Judgment Day captures on film a landmark court case with a powerful scientific message at its core. Evolution is one of the most essential and least understood of all scientific theories, the foundation of biological science. We felt it was important for NOVA to do this program to heighten the public understanding of what constitutes science and what does not, and therefore, what is acceptable for inclusion in the science curriculum in our public schools.
For more information, see the article "Is Intelligent Design Science or Religion?"