Most boat floors are nothing but 3/8" plywood, many manufacturers do nothing to protect the under side of the wood, and worse yet, most carpet the top side which holds water and contributes to the rotted wood. The best floors are gelcoated and totally sealed with no carpet, they can be hosed down and washed up easily. Those are normally found in boats intended for fishing.
Most fish and ski, and cuddy cabin boats are carpeted. If the floor is rotted or soft, chances are it's been stored outdoors and it's been wet, the floor is rarely the only problem, the lower supports, stringers, and wood in the transom can also be rotted if the boat was not kept dry. Most boats are also foam filled, that foam gets wet and holds moisture, which in turn adds the the rot problem down below. Your best bet is to do a very thorough inspection on any boat you intend to buy, and then decide whether or not it's worth the work to repair it if it does need work. If you have to pay a marina to do the work, its going to be expensive. If you are not up to doing the work yourself, it's most likely not worth it for you to buy one that needs that sort of work.
Many newer boats are built wood free, using all aluminum and composites that do not rot. Those also hold their value much better.
