We don't know why they were boarded. We don't know the circumstances because the article doesn't provide the details. Conclusion of many is all based on conjecture of the few comments of two men in this article.
"In addition to trying to ensure the safety of boats on the bay during the holiday weekend, Warren said, the operation was part of an effort to increase the public's awareness of the Coast Guard's role as a law enforcement agency under the Department of Homeland Security. He said the public might have been surprised to see weaponry that is now standard issue to all Homeland Security forces."
I think that says it all. Furthermore if these guys had been terrorists the papers would've all been touting their arrests--no arrests were made. So I reiterate:
If you want to fight Islamic terrorists go to a FREAKING MOSQUE and leave decent American citizens alone.