The Portuguese winger was sent off for violent conduct at Portsmouth on Wednesday and while Ferguson had no quibbles about the red card, he believes his player was provoked by a series of heavy challenges that went unpunished by referee Steve Bennett.
"My fear is, and I don't whether there is a directive, but maybe referees are a bit more tolerant of the physical contact," Ferguson told reporters on Friday.
"I've noticed this in the last few months -- late challenges are going unpunished. I thought these things were black and white. Late challenges are not allowed.
"We saw it again on Wednesday night, the referee letting it go unpunished time and time again. If you have got weak referees then you are going to be suffering."
Ferguson added: "There is a concern players like Ronaldo are going to be the victims... because it will end up with someone getting a serious injury."
The fiery Scot had every sympathy with Ronaldo, who was dismissed for an apparent headbutt in the closing stages of the 1-1 draw.
"It's very difficult to completely punish Ronaldo or be angry with him," Ferguson said. "Some of the things that are happening to him are not right."
After opening with two draws they already trail Chelsea [ Images ] and Manchester City, who have taken maximum points under new manager Sven-Goran Eriksson, by four points.
"We are dropping points and that's frustrating because the performance levels were very good," Ferguson added. "The important thing is just to be patient now.
"The players will come right. It's frustrating, but it's recoverable of course."