There isn't one material that is best for all types of fitness flooring under all circumstances, but what follows should help you make the right choice:
Rubber remains one of the most popular choices for good reasons. it is resilient and strong. It can accommodate just about any type of equipment or exercise. Rubber is also easy to fit and maintain, shock-absorbent, water-resistant and it provides reasonably good soundproofing.
Rubber does have a few cons, however. It is e.g. relatively expensive and fairly heavy.
For floor-based exercises such as pilates and yoga, this is no doubt the most comfortable option. Foam is versatile and provides great cushioning and comfort. It also comes in a variety of styles and colors.
The cons are that, because it is less durable than other options, it has a relatively short lifespan. It is also a magnet for sweat and dirt and it is unsuitable for heavy fitness equipment.
Vinyl can withstand a lot of heavy use, yet it is a comfortable and stylish option. It is also moisture, mildew, and mold resistant. And when the time comes to clean up all that blood, sweat, tears, vinyl is easy to clean.
The downside is that vinyl has a low shock absorbency and it can easily be damaged by sharp objects. Another concern is that there might be a relatively small health risk of VOC emissions.