Ryan Cresswell got the ball rolling for the Shrimpers before before in-form forward Gavin Tomlin made it 11 goals in 10 games with a brace of second-half headers.
"We got beaten by a lot better team," said Cook. "They were a lot more powerful and hungry, they had strength all over the pitch and you could see they wanted to win.
"We seemed to lack a bit of physical presence in the team. We started okay in the second half but, after Southend got the two quick goals, the game was already over for us.
"We were looking for leaders on the pitch to stand up and fight but we didn't have any.
"We will go forward and carry on trying to get promotion - we need to make sure we collect points over the Christmas period if we want to be up there.
"Southend are one of the strongest teams we have come up against this season and they have set us a benchmark if we want to be competing near the top."