Apple has the craftsmanship (and to an extent, innovation) credentials, but Microsoft's products were more flexible due to their focus on software instead of developing both software and hardware. As someone mentioned, they offered the flexibility most people back in the day desired for both the office and the home. Apple was less willing to concede to such demands, you had to buy the full package, so to speak. Plus, the marketing was different: Microsoft was rather upfront even in the pre-Windows era about catering "to the average Joe", while Jobs and other Apple bigwigs often focused on presenting the technological trickery of their latest products (in a kind of vaudevillian way).
Ultimately, unless Apple leadership/management gets a change in an ATL, and becomes more flexible earlier on when it comes to questions of developing software and hardware in a less interdependent way, some ATL company will simply fill in Microsoft's niche (to varying degrees). Or, if Apple undergoes such changes in an ATL, it itself could become something of an ATL Microsoft, funnily enough ! (Not necessarily in a fully comparable manner, especially if it keeps its focus on developing hardware as well from early on, instead of returning to it later.)
Ultimately, unless Apple leadership/management gets a change in an ATL, and becomes more flexible earlier on when it comes to questions of developing software and hardware in a less interdependent way, some ATL company will simply fill in Microsoft's niche (to varying degrees). Or, if Apple undergoes such changes in an ATL, it itself could become something of an ATL Microsoft, funnily enough ! (Not necessarily in a fully comparable manner, especially if it keeps its focus on developing hardware as well from early on, instead of returning to it later.)