Retired FDNY firefighter Tim Brown launched a national petition drive and helped organize the rally to challenge the decision.
"We don't agree that these murderous terrorists are afforded the same rights as our nation's citizens under our Constitution," he said.
Demonstrators at the Saturday event included the actor Brian Dennehy and a number of people who lost friends and relatives in the 9/11 attacks.
Anger at the Obama administration ran hot in the crowd. One person held up a sign calling Attorney General Eric Holder "disgraceful and despicable." Another sign said "Obama/Holder ... Jihad from within."
Former U.S. attorney general David Kelly believes federal court is more effective than military tribunals, but some New Yorkers fear the proceedings will make the city a target for terrorism.
Addressing the crowd, Dennehy passed along a message from the father of murdered Wall Street Journal reporter Daniel Pearl, who is opposed to a public trial for reputed terror mastermind Khalid Sheik Mohammed.
The actor said he also believed the trial would be "an uncalled-for ordeal that could be used for political purposes."
"This will provide the radicals with a huge forum," he said. "Why should they have the normal constitutional protections?"
Lee Ielpi, a retired firefighter whose son, also a firefighter, died on 9/11, said he believed the U.S. has been in a state of war since the attacks, and that a military tribunal was therefore the appropriate venue for justice.
"They deserve a fair trial in a military tribunal, not on our soil," he said. "Guantanamo is where it should be."
Other victims of the attacks disagreed.
Lorie Van Auken, who lost her husband at the World Trade Center, said in an interview before the rally that it was fitting that the accused answer charges a short walk from ground zero.
Another supporter of the trial plan, U.S. Rep. Jerrold Nadler, said military commissions have a poor track record when it comes to convicting terrorism suspects. The New York Democrat expressed confidence that U.S. prosecutors can win a conviction in a regular, civilian court.
On November 24, NYPD Inspector Michael Blake, the man responsible for the security considerations for the terror trial was promoted to Deputy Chief.
In prepared remarks, Commissioner Kelly said Blake has already conducted a preliminary assessment of locations that will be affected by the trial, including the federal courthouse at 500 Pearl St., the Manhattan Detention Center, and surrounding streets and buildings.
Blake, who is 48 years old, joined the force in 1986.
The already controversial trials became more so after a defense lawyer said the proceedings will allow the defendants to spout criticism of U.S. foreign policy.
The attorney for one of the defendants announced the five suspects would all plead not guilty, including Khalid Sheikh Mohammed, self-proclaimed mastermind of the attacks.
The attorney said the terror suspects would not deny their roles in the attack, but would explain "what they did, and why they did it" – using the trial as a political platform to criticize U.S. foreign policy.
Holder's critics have pushed for the alleged plotters to be tried before a less public military commission, which would have also allowed for a more flexible standard of evidence, and, they say, a safer environment.
Legal observers say while a federal civilian trial will not exactly provide them with an open ended opportunity for full blown propaganda speeches, the suspects may be heard on some level.
Defense attorney Brian Neary, who is not involved with the terror trial, says political banter will have no place and no effect in federal court.
"Politics is generally not one of those things that's considered a defense," Neary said. "Once they get to the penalty phase – whether or not they'll be imposed the death penalty – they may have an opportunity to present their views much more free-wielding.
"But it's not, again, a political opportunity for them to make a speech against America or on behalf of their own political concerns," Neary said.