It's a natural consequence of a certain situation; it's something to be expected. “It goes” may be used as well

You cannot always complain about injuries: you are a rugby player! You know that jnjuries come with the territory

Non puoi lamentarti in continuazione: sei un rugbista, lo sai che infortuni e dolori sono rischi del mestiere

I'm the sales manager now and have to travel an awful lot even when I don't feel like it. But, I guess it comes with the job

Ora sono il direttore vendite e viaggio moltissimo, anche quando non ne avrei voglia, ma fa parte del lavoro e va messo in conto

Professor Brown owns lots of books; the walls of his house are covered with them! But then, being a college professor of literature, I guess it comes with the job

Il professor Brown possiede una marea di libri, le pareti di casa sua sono ricoperte di libri, cosa che va messa in conto visto che è un docente universitario di letteratura

This expression originally referred to sales personnel who had to accept whatever problems or situations they would find in their assigned "territory", i.e. sales district