There may be much happening in the background that we aren’t aware of; at least I hope that’s the case. At any rate, the Muslim chaplains appear to have been under investigation way before this arrest.
Here's an interesting tidbit from the statement by the Al-Arian supporters, the Tampa Bay Coalition for Justice and Peace, on March 28, 2002:
...on March 20th, federal authorities raided over 16 Muslim institutions and homes of prominent Muslim leaders. The name of Dr. Al-Arian appeared on the search warrants of these raids. The reasons for Dr. Al-Arian’s name or the raids have absolutely nothing to do with the September 11th attacks or with security. Dr. Al-Arian had never even heard of 11 of these organizations. On the other hand, one of these organizations, namely the Fiqh Council of North America, is the highest Muslim religious authority in the US. It’s concerned only with religious opinions, which are considered very moderate. The Graduate School of Islamic and Social Studies (GSISS) which was also raided, is the official certified school for endorsing Muslim chaplains by the Defense department. Of the 13 Muslim chaplains in the different military branches, 9 were graduates of this school.
Note also that on the same website, academicfreespeech.com, there’s a letter of support for Al Arian from none other than Vincent Cannistraro, former CIA chief of Counter Terrorism. Cannistraro is frequently quoted in the NYT and other birdcage liners. Is it any wonder why we are in this mess?