If the loss to the well pump is from a covered peril, then yes, it will be covered! Most common losses come from lighting strikes, fires, or windstorms, which are all things typically covered by your homeowners policy.
If it fails due to normal wear and tear, then the home policy won’t provide coverage. I suggest checking the manufacturer’s warranty; you may find additional protection there!
For more information about well pump coverage, check out this article: How to Tell if Your Home Insurance Covers Well Pumps.