My father commutes to work on the seven o'clock subway.
Literal
Father [topic-は] company [toward-へ] seven-o'clock subway [by-で] is-commuting.
通っている uses ている for a habitual action — 'commutes regularly.' The の in 七時の地下鉄 turns the time into a modifier. Three particles doing different work: へ (direction), の (modification), で (means of transport).