Part of it may also be who your travel agent is booking the tour through. They may have a couple of trusted tour operators and only use them for your particular destination. I once sent a 10 day customized itinerary in East Africa for a customer to approx 10 different operators. The big name ones that have offices, brochures and bonding in the USA came back almost double the price of a smaller outfit who only promotes himself in Tanzania other than a website. His outgoings are so much smaller, and so his mark up was also.
The one thing that made me as an agent uncomfortable selling this company to my client was that he has no established business in the States. If he had took my clients money and ran with it, there would have been no way to get that money back, report him to the BBB etc, and as agent my customer is looking to me to steer him in the right direction. In the end, I offered him the identical itineraries with the huge price difference, shared with him the reasons why and my concerns and then left it to my client to make the decision for himself. He opted for the least expensive guy, and he had a fantastic time, at half the price.
One word of advice for doing it this way: Every country has a tourist board operated by their government that above-board tour operators will register with. I would save yourself the money and go with the lower priced company that doesnt have to pay for offices abroad and fancy brochures, once you have checked them out that they are at least registered as a Bonafide company in their home land. I had done this for my customer prior to offering him the small company and it was a happy ending for all.