On the locking the bike up in the car - yes, especially if it is sitting there all day. Our DS had his bike stolen out of the back of his pickup truck - he has a shell and it was locked but they forced the lock and took his bike...
Our bikes have fenders and racks. Due to fenders they won't fit in our bike rack so we load both bikes into the car - Our station wagon is more of a truck now than a car
we have given up on protecting the carpet but we do put a blanket between the bikes and we make sure nothing is rubbing the roof of the car and protect if it is. We also take our bandana's and wrap our leather saddles in case they are rubbing against anything - to protect the saddle.