Hernandez, a non-roster invitee, will instead compete for a bullpen job.
"He's out of the picture as a starter," Cooper said. "I just told him, 'Look, the performance we saw [on Saturday] and what I've seen in the past, it just wasn't what we thought it would be.' We just don't have the innings to keep things going, so we want to give him an opportunity in the bullpen. He might fit in there."
Hernandez has allowed 11 earned runs over 10 1/3 innings this spring, spanning four outings. He yielded three home runs and walked seven while striking out five.
In his most recent outing, on Saturday in Winter Haven, Fla., he yielded six runs, including two home runs, over three innings.
"We want to see him have a chance," Cooper said. "Staying true to form, that's what we've talked about -- 'x' number of guys get a chance for the rotation and will be evaluated. That's what we've done. We like his arm, no question of that."
"That's not the way I want it, but that's the decision that was made," Hernandez said. "I'll take it not the wrong way, but in a good way. Everybody knows I've got a strong arm. No matter where I'm going to be, I want to be part of this team."
The pool of rotation candidates now stands at seven: Roy Oswalt, Woody Williams, Brandon Backe, Chris Sampson, Shawn Chacon, Jack Cassel and Wandy Rodriguez. Brian Moehler is also being stretched out to start, but he has less of a chance to make the rotation than the others.
Though several pitchers have been eliminated from the running since the beginning of Spring Training, poor performances have been a staff-wide issue. Part of the inconsistency can be attributed to injuries, but some pitchers have simply not been very good this spring.
Of the 21 pitchers who are presumably healthy and still in Major League camp, only eight have ERAs under 5.00: Oswalt (2.40), Backe (4.00), Moehler (4.15), Dave Borkowski (2.57), Oscar Villarreal (0.00), Carlos Hines (0.00), Wesley Wright (1.35) and Ryan Houston (3.00).
Several pitchers who were considered locks to make the team have struggled, including Doug Brocail (19.50), Geoff Geary (5.40) and Shawn Chacon (10.12).
Cooper said that he's not worried about the quality of the pitchers, though he is somewhat disappointed that the competition for jobs wasn't as fierce as he expected it would be when camp began.
"I'm more concerned about health," Cooper said. "I'm disappointed [Felipe] Paulino was injured and [Fernando] Nieve was injured. I would have liked to have seen these guys we've had in that running just step up and make that competition really good. We haven't had it.
"We're down to, at this point, seven, eight guys. We had 11, 12 when we started out. Our pitching's good, but we haven't had the competition I'd thought we'd have. That's the only disappointing part. I think we still have depth, I think we're still good. I think we have the guys here to get it done. The injury thing kind of concerns me a little bit."
Alyson Footer is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.