Rooney was pelted with coins and objects, at one stage calling referee Michael Oliver over before he took a corner and pointed out a coin on the pitch.
The official picked up the coin and got the game under way.
"I don't think it'll bother Wayne at all," he said. "I'm sure all those people who were throwing will be cheering him on in three months' time."
Moyes was full of praise for Rooney's goal in the 2-0 victory at Selhurst Park.
"When he's not got time to think he does things naturally," Moyes said.
"The ability to get his weight behind the ball, strike it cleanly, was good. Some of his passing was fantastic."
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