There are three main reasons that your floor might be cold.
1. Not enough insulation.
3. Not enough heat.
To solve the problem, you’ll need to find out which of the three things is the problem (or maybe it’s all three).
Start by taking a look under the home at the insulation levels. If your home is built on a slab, you can skip this step. Get a face mask, some old clothes, gloves, eye protection (things will probably fall on your face), and a flashlight. Is there insulation under the floor? The insulation should be to the full depth of the floor joists, in contact with the floor, and intact (no rodent or water damage).
While you are down there, look at the places where stuff goes through the floor – plumbing, electrical, and duct work. These penetrations should be sealed with some kind of foam, with no gaps or holes. Look at the ducts as well, if your home has them. Are they all connected? Are the seams on the metal ducts covered with mastic? Are they insulated? Are the junctions on the flex ducts connected with large zip-ties? There should be one on the inner sleeve and one on the outer sleeve.
Finally, look around for water damage – rotten wood, water lines on the walls, standing pools of water. The crawl should be dry, with a layer of black plastic sheeting on the floor.
Head back inside. If the floor looks good (full insulation, no gaps at the penetrations, ducts sealed and insulated, no water), then the problem might be drafts coming from elsewhere in the home.
Warm air tends to travel up – causing a higher pressure at the top of your home and a slight vacuum at the bottom. If your floor is well air sealed and insulated but the ceiling or walls are not, you will still have drafts.
In addition, large cold areas on the walls (like windows) will cool off the air, which gets heavy, drops to the floor, and pulls more warm air to the top of the window – a process called convective looping. If you put your hand on the base of a window and feel cool air moving gently and consistently, this is most likely the effect that your are feeling.
The final thing to think about is the amount of heat being produced in the home. Even a well insulated home with the heater turned too low will get cold and uncomfortable. It can be a balancing act between heating the whole house all the time (using more energy but being more comfortable) and heating parts of the house part of the time (using less energy, usually, but being less comfortable). If this is the case, either crank up the heat or insulate and air seal the rest of the home so you can use less heat to be more comfortable.