The larger goal was uniting Americans around the war effort.
Cracking down on dissent would be a negative action in support of the larger, positive goal the government sought. The government wanted a fully united public in support of the war, and so it put out the message that that freedom of speech might have its limits in times of war.
The Patriot Act was highly controversial because it restricted and limited many American freedoms, such as Habeas Corpus. It also enacted a number of surveillance measures.
<span />