Apple and Google have a duopoly in the mobile app distribution market, and they're abusing that duopoly in an anticompetitive manner to prevent companies from competing with them in mobile app distribution. Anti-trust legislation gives regulators the right to order and prosecute companies for abusing their market positions and for limiting the ability of the free market to deliver to consumers better, more efficient and less costly solutions.

Microsoft in the late 1990's and early 2000's was in a similar situation. They abused their position in the PC operating system market in an anticompetitive manner to prevent competition in the browser market[1]. Microsoft built their OS and Internet Explorer, so who has the right to tell them what they can and cannot do with them? It turns out that the federal government and regulators around the world have that right.

This is like asking why regulators have right to prevent Standard Oil from engaging in anticompetitive behavior, given that Standard Oil built their own pipelines and railroads, after all.

[1] https://en.wikipedia.org/wiki/United_States_v._Microsoft_Cor....