Knowledge has been lost
In the middle of the experiment that created Captain America, the Dr. Erskine, the German scientist leading the project (Stanley Tucci), was killed by a Nazi assassin. Because of poor "bus factor", the knowledge of how to reproduce the experiment at scale died with Dr. Erskine.
Col. Philips was frustrated by the huge setback in the project.
Col. Philips wanted to send Captain America to Alamogordo to assist other scientists in trying to reconstruct Dr. Erskine's work, a role which would basically consist of being a "lab rat".
The context was "going to Germany to fight HYDRA"
"You are not enough" means that Philips wanted more than one soldier to square off against HYDRA.
Col. Chester Philips: I spoke to the president this morning. As of today, the SSR is being re-tasked. We are taking the fight to HYDRA. Pack your bags, Agent Carter. You too, Stark. We're flying to London tonight.
Steve Rogers: Sir, if you're going after Schmidt, I want in.
Col. Chester Phillips: You're an experiment. You're going to Alamogordo.
Steve Rogers: The serum worked.
Col. Chester Phillips: I asked for an army and all I got was you. You are not enough.
... (to fight HYDRA).