Yes. This I think is a downside of the law. Some small owners are going to have a more difficult time.
But this is true for any regulation like food safety regulations, construction regulations, etc. They hurt more a small restaurant than a big chain. But in the end, these regulations are there to protect the customers. Small restaurants have closed and will continue closing for not following food safety regulations. But what is the alternative? Is business creation the final goal of our society? Or there are things more important?
In summary, small businesses are going to have to extend their insurances to also cover risks related to GDPR. But it's the price to pay for having safer data.