LÁZARO CÁRDENAS, Mexico—Naum Rosas runs a fleet of 30 vans that ferry workers between this busy Pacific port city and surrounding villages. Until recently, when he wanted to raise fares, he didn’t go to city hall. He cleared it with gang bosses.

If Mr. Rosas refused to deliver a percentage of profits to them, or take his vans to carwash businesses run by gang members, he was warned that thugs could torch his vehicles—even with the passengers inside.

“We...