It's a startup that does online booking for transit advertising. I assume Radio FM advertisers and newspaper advertisers as my target audience. So, how can I reach them? Do I contact advertising agencies or directly reach brand owners/marketing department?
I've spent many years working in a marketing department as our primary brand liaison to the advertising agency. Based on that, I believe you need to strongly consider both as your target audience.
I suggest developing a relationship with the media buyers/planners in agencies. When they do need transit advertising as part campaign their agency is developing, they will think of your company because of the relationship you have developed. Additionally building relationships within the marketing communications/brand owners will also be helpful. Every business/corporation is different. Some may have their own media buyers on staff, others may rely on their agencies to make the buy but they can influence what media is bought on their behalf (or direct who the agency should work with at a specific media outlet).
My gutt tells me you should focus your energies on the media buyers at agencies, with the brand owners/marketing departments as a secondary focus. My rationale on that is solely from my personal experience. If I were in the position to buy transit advertising, it wouldn't be something I did often so I would go back to the agency for assistance to make sure I was making a good decision and negotiating the buy for the best outcome.
I'd be happy to discuss further if you have additional questions. Good luck!