The ferry is safe but try to time it so the boat you get is the Coastal Renaissance. Two reasons
1) Its a great boat to take your car on. Everything below deck is brand new, everything is wide and solid. You have little reason to worry
2) Its gorgeous on deck. Much better than the Queen of Coquitlam or whatever normal service vessel they have on duty. She should experience it properly.
Tofino is a few hours from the Nanaimo ferry so, weather permitting, (The highway between Port Alberni and Qualicum can get shut down if it snows) make sure that you don't spend too long on the isle. Budget a full day (come over on the 6am sailing) and come back on the last sailing (9pm) or stay overnight in Victoria and take the Sidney/Swartz Bay boat to Tsawassen.
DON'T GO NORTH OF QUALICUM ON THE ISLAND HIGHWAY! THERE IS NOTHING TO SEE THERE! IT IS A BARREN WASTELAND!
Have you ever seen the movies Mad Max, Doomsday, or The Road?
Yeah, its like that.