The Hardball anchor suggested the attacks might have been set up or staged, in the hope of undermining Democratic claims that Russian hacking and espionage swung the 2016 US Presidential election in Mr Trump's favour.
He is contradicted by a spokesperson for Russian President Vladimir Putin, who said the assault would "inflict major damage on US-Russia ties".
An agreement to prevent clashes between Russia and America in Syrian airspace has now been suspended by the Kremlin, in response to the cruise missile bombardment which destroyed at least nine jets in a Syrian airbase.
Launched in response to an apparent chemical weapon attack on a rebel-held town, which left over 80 people dead, it was the first direct assault on President Assad's forces by the United States since the outbreak of civil war six years ago.
President Trump said he hoped to "deter the spread and use of deadly chemical weapons" like the sarin or chlorine allegedly used in the "barbaric" bombing.
But speaking on MSNBC, veteran analyst Chris Matthews said: "Maybe it's cynicism but i thought... if there was a way for [Mr Trump] to kill the narrative he's in bed with Putin it would be this.
"Take on Putin's warm freshwater port [in Tartus], take on his satellite, his loyal ally Assad. And that would be a way of saying I was never in bed with this guy, i never planned any kind of coalition in Moscow."
The Russian naval base in Tartus gives Mr Putin vital access to the Eastern Mediterranean basin, allowing for Russian warships and submarines to pass from the Black Sea into Western waters and potentially providing a route to untapped natural gas resources.
It's the only Russian naval base on foreign soil, and maintaining control of Tartus was perhaps the principal reason for Mr Putin's entry into the Syrian arena of war.
Mr Matthews continued to speculate that Mr Trump and Mr Putin may have "have had a phone-call this evening, and they worked this thing out, and it was a set piece that was not meant to be particularly antagonistic to Moscow."
Russian forces were admittedly warned of the strikes 30 minutes before they took place, using the so-called "deconfliction line" used to prevent clashes between the two superpowers in Syrian airspace.
No Russian casualties have been reported, though their personnel were stationed on the base where six Syrian soldiers lost their lives, along with nine civilians in a neighbouring village.
But Mr Putin has now suspended the deal to prevent conflict between American and Russian forces and called for a UN security council meeting to discuss the strikes.
Kremlin spokesperson Dmitry Peskov said President Vladimir Putin considers the strikes an "act of aggression" made on a "made-up pretext". He said the strikes would "inflict major damage on US-Russia ties", and suggested they were intended as a distraction from mass civilian deaths allegedly caused by US bombing in Iraq.