Nixon is under investigation by the AFLPA's agent accreditation board after admitting to having had "inappropriate dealings" with the 17-year-old girl at the centre of the St Kilda nude photos scandal.
"I don't have all the facts and I don't think anyone's got all the facts, [but] on the surface it doesn't look great," Malthouse told SEN Radio on Thursday.
"The thing about this is it's not the players he currently has [that are the issue], it's when he knocks on the door and says to a parent 'I'll look after your son and take him through his 10 or 12 years of football'.
"Parents will question all that regardless of what evidence they've got. I'm not going to point the finger at Ricky because we know what we read, but do we read everything that's right?
"Everyone is doubtful about that anyway because it’s generally the case that no one has the full facts, but as a parent that's going to be the issue.
"On the surface it doesn't look great for the future."
