I have a large Specialized Sirrus commuter bike with fenders, back rack with trunk, side mirror, elevated flat bars, etc. and it takes up a lot of room.
I have put it in the back with the wheel off using a front fork clamp attached to a board, but it's difficult to get it in and out.
My newest solution is to put it in sideways behind the front seats at an angle. I know others have done this, but I thought I would share my procedure:
Fold the back seat bottoms up vertically.
Tilt the drivers seat forward
Slide the passenger seat all the way forward and tilt it forward all the way.
Open both back doors and the right front door
Take the front wheel off the bike
With one leg in the car from the right side, roll the back of the bike in and get the handle bars in.
Lift the back wheel over the left door jamb and partly out the left door while getting the front of the bike inside and angling the front forks forward toward the back of the passenger seat door.
Once you get it in this position you should be able to close all the doors.
Tilt the passenger seat back so that you can see the right side view mirror while driving.
Tilt the drivers seat back to what is comfortable, mine is slid all the way back with no interference with the bike.
Put the front wheel where ever you want, I put it as shown in the photos leaning against the right back vertical bottom seat.
This is obviously a one bike setup, but I like it because it is so easy and quick to get the bike in and out, the bike is secure inside the locked car, you can put a tarp down on the back floor if the tires are dirty or muddy so you aren't making a mess in the back hatch area. There is still room for a passenger, tight with my bike because of the front fender, but still possible. And.. it's free!
I've been putting my 64cm Atlantis in the back of a Mazda Protege, but it's coming up on 200,000 miles and I'm thinking about a Fit. Sometime in the next couple of days, I plan to wheel the bike into the Honda store and see what works...
I have a Fit as well but I think it is much easier to take the front tire off and clamp it in the back as you said. That's what I do with my bike and it stays in my ride all the time. In fact, I even leave the back passenger seat down so I can run my two kids around town when necessary (one in the front seat and one in the back). It seems like a bit more effort to have to push the front seat up and back.