Microsoft shipping IE in Windows did not ruin companies.
What ruined companies (and what MS was actually prosecuted for) was Microsoft telling PC manufacturers "we will only sell you Windows OS if you agree to NOT install any other browsers on your computers." Those agreements were how MS abused their OS monopoly to wrongfully exclude other browsers from the market. Up to that point, Netscape was selling their browser direct to Dell, HP, Gateway, etc. to be preloaded on machines they sold.
Microsoft was a supplier to PC companies and the market they distorted was the software supplier market. Apple themselves are the device manufacturer and have under 50% share in that market; it's not a comparable situation.