There are several limitations of free WordPress.com which differentiate it from WordPress.org. Here are some of the disadvantages of using WordPress.com:
They place ads on all free websites. So your users will see ads, and you don’t make money from it. If you don’t want your users to see their ads, then you can upgrade to a paid plan (starting from $36 per year).
You are NOT allowed to sell ads on your website. If you run a high traffic site, then you can apply for their advertising program called WordAds where you share revenue with them. Premium and Business plan users can use WordAds right away.
You cannot upload plugins. Free plan users get built-in JetPack features pre-activated. Business plan users can install from a selection of compatible plugins ($299 / year). WordPress.com VIP program lets you install plugins, and it starts from $5000 per month.
You cannot upload custom themes. Free plan users can only install from the limited free themes collection. Premium and business plan users can also select premium themes. There are limited customization options for the free version. Premium and Business plan users can use custom CSS.
You are restricted to their stats. You cannot add Google Analytics or install any other powerful tracking platform. Business plan users can install Google Analytics.
They can delete your site at anytime if they think it violates their Terms of Service.
Your site will display a powered by WordPress.com link. It can be removed by upgrading to the Business plan.
WordPress.com does not offer any eCommerce features or integrated payment gateways.
You cannot build membership websites with WordPress.com.