They feel threatened by hands reaching in at their eye level, and they may lunge at or bite the intruder. Some people prefer side doors because it's easy for the rabbit to hop in and out on his own. You can make a top opening cage easy and safe for your rabbit to jump into and out of by draping a towel across the top when the cage is open. This gives them a fairly solid surface for takeoffs and landings, and prevents them from getting a toe or foot caught in wire. The size of the door is also worth noting.
Many cages have doors that are too small to fit a litterbox.
You can enlarge a door on a store-bought cage using wire cutters and crimpers. In general slatted floors are easier to clean and easier on your rabbit's feet. Dwarf rabbits and very young rabbits sometimes have difficulty on slatted floors because their feet can become caught between the slats. A wire floor should be at least partly covered by newspaper, wood, cardboard, or a towel, to give the rabbit a chance to rest on some surface other than wire. A litterbox inside a wire cage also serves this purpose.