We can tell a lot from the size/shape of bones and scars where sinew and muscle was attached. How fast an extinct animal was likely to move is just one of a host of information gathered from fossils.
Modern horses can certainly run a lot faster than their ancestors but have been bred to do so domestically for 4000 years so can not fairly be compared with their much smaller wild ancestors.
When dealing with domesticated species it is important to differentiate between wild (as in not genetically altered by selective breeding) and feral animals. The only true wild horse left is the przewalskii which is a small stocky animal barely 13 hands high.