Yeah, I know this sounds cynical but it's also true. When you make the decision to work for yourself, either freelancing or running your own company, you’ll end up doing less of what inspired you in the first place. That’s not to say you won’t learn to love all the new skills and duties essential to running a company but you can expect to spend 75% of your time finding work (and everything else related to running a business) and 25% of your time getting your hands dirty with creative work.
When I first began art directing it took me awhile to realize all my years of training as a designer were still relevant but I really needed to begin investing in a new set of skills related to management. Working for yourself is similar but you don't have someone, a manager or director, telling you what to do. It's all up to you and that requires some extra initiative and discipline.
Is the autonomy worth it? For some entrepreneurial folks, of course it is. But some people would rather focus on making stuff and letting others handle the contracts, invoicing, biz development, etc. What kind of person are you? In either case, there are tons of tools out there to help you manage yourself and your business. Find and master the business tools that let you spend more time making stuff and less time managing stuff.