Of course, the most obvious difference between these two types of workplaces was their scale. Factories were much bigger than small workshops. However, this is probably not the most important difference. The most important difference, I would argue, was in the different ways in which workers experienced each work place.
In a small workshop, the worker was more like a family member than an employee. The owner of the shop and the workers tended to work side by side on the same jobs. The owner might be grooming one or more workers to take over the shop or to set out on their own. This was a relatively egalitarian system in which people were treated as people.
In a factory, by contrast, there was very little in the way of human relationships. The workers were simply workers. They were similar to the parts of the machines they worked with. Because of this, they would have experienced their work as a much more negative and impersonal thing than they would have when they worked in small workshops.
Overall, then, the biggest difference is that factories were impersonal places where a worker was just a worker, not a human being who was important for their own sake.