Arthur Leigh Allen almost certainly was not the Zodiac. He's been disqualified on the basis of handwriting, fingerprints, palm prints, and a comparison against a partial nuclear DNA profile extracted from one of the letters.
He is a popular suspect because he was the prime suspect given in Robert Graysmith's book "Zodiac" (1986), and the movie "Zodiac" (2007), which was primarily based on the book. However, most who are familiar with the case no longer believe Allen was the Zodiac.
In case you're interested, here is a collection of people accused of being the Zodiac:
http://zodiacrevisited.com/people-accused-of-being-the-zodiac-killer/