You are raising an interesting point.. Why do you want to deal directly with charter company ? To get better price
? To play safer ? If so, dealing directly with the charter company doesn't assure any of them. Most of the charter companies do not offer better prices than the agencies will do. If they do, there will be no more agencies working for them and there is no charter company that can rely only on their direct sales.
On the other hand, if the charter company is not the right one, you can always run into trouble, whatever way you book. Actually, if you go through a agency, provided that these are someone that you know and trust, there is less risk. Moreover, the agencies can also help in organising the flights, transfers, etc and more importantly as they are working with many other charter companies for years, they can tell you better which one is more reliable.
Don't get me wrong, I am not advocating neither way; I am running a charter business and 60 % of our bookings are direct bookings. But unless you are 100 % sure that you know the company well, you don't need any other service
and you believe that booking directly would be cheaper, go through agencies.
Be aware though.. Some of the agencies are kind of ashamed of being seen as an intermediate commissionaire and they advertise themselves as a charter company. I have seen on internet
some companies that are telling that our base and our boats are their own !!!
So, if possible, find an agency in yr country, talk to them or meet them in boat shows, etc and if you are convinced , go ahead.