Metatarsalgia is a bad term for a common problem in runners. It is a term that unfortunately gets used a lot but is quite a meaningless term and diagnosis. The term is like, for example, saying you have a sore knee. That sore knee could be due to any one of multiple different things. Metatarsalgia means pain in the metatarsals or forefoot, so it can be due to multiple different things. That is why the term is so meaningless.
The cause of the symptoms could be a callus of the skin under the ball of the foot; it could be a pinched nerve that causes shooting type pains; it could be a fat pad atrophy that causes problems with weight bearing; or it could be arthritis type symptoms inside the joints in the ball of the foot. Each of these potential reasons for metatarsalgia are very different to each other with different symptoms and different causes which just serves to illustrate just what a poor term it is to use.
Probably the most common cause for pain in the ball of the foot is a condition called a plantar plate tear. This is a strain of the ligament under the joints in the ball of the foot that can progress to a small tear. The pain is typically over the joint on the bottom of the foot and just distal to the joint. Usually it is the second metatarsophalangeal joint, but it can affect all or any of the joints. It is more common in those who exercise more. It starts as a mild ache that is often ignored, but it will progress unless there is a treatment started as it does not heal on its own.
Typically the treatment of a plantar plate tear is to use strapping to hold the toe in a plantarflexed or downward position to prevent it from bending up so the strain is given a rest. A rocker sole shoe or a shoe that is stiffer can also help do this. If this helps, it does tend to take a long time and patience is needed. If it does not help, then some plantar plate tears need a surgical treatment.