Yes, I would start the space pretty small and slowly expand it. I gave my bun too much space too quick and he started to have accidents. I started over and very slowly increased his space and he did much better. I still cannot leave him unattended when he is free roaming but he is great in his pen.
I would get something to put on the tile. For a little bit of cushion and traction. Walmart has really cheap area rugs/runners. That is usually what I get. As far as the hutch flooring I personally would get those rubber mats that lock together covered with a incontinence pad, towel or fleece. If your bunny may have accidents then I would go for the incontinence pad (if he wont chew it).
I use these in both my buns pen and cage and LOVE them – http://www.amazon.com/EZwhelp-Washable-Whelping-Puppy-Pad/dp/B003B3W6C8/ref=sr_1_1?ie=UTF8&qid=1386708596&sr=8-1&keywords=whelp+pad.
They are a quilted material so you can’t just brush them off like a sheet but they wash really well and are very absorbent. I was using disposable puppy pads and it was costing me a fortune. For the cage I have the plastic bottom, a couple towels for cushion then the whelp pad on top. For the pen I have carpet, a heavy duty shower curtain (2) and the whelp pad on top.
For the litter box I am using newspaper to cover the bottom, then shredded newspaper then wood stove pellets sprinkled around to help with odor and to absorb the pee. I change the boxes (2) every 3rd day so it is working well for me and it is cheap.