Their nuances are different, and you need to decide each time which is appropriate.
When を is used:
秘書を伴って: You are the main person, and your secretary is accompanying you.
危険を伴う手術: The main event is surgery, and some danger comes with the surgery.
When に is used:
父に伴って: Dad is the main person, and you are accompanying him.
人口増加に伴う住宅問題: The main (first) event is population growth, then housing problem comes after that.