Whelan said that young managers need support, not interference, based on his experience with Steve Bruce and Roberto Martínez.
"Zola has done a good job under difficult circumstances," Whelan said. "He has had to deal with injuries and financial problems and I don't know what has gone on with the new owners. But he needs to be supported and helped.
"I've had a similar situation with Roberto. He is a young manager who has come up from the Championship. We've had our disagreements, most recently when we drew against Portsmouth but it's his job to make the team work and I have to respect that."