When you start a company, you choose a "tax year" by filing a tax return. From then on out, you file your tax return the same month every year.

If it's a small business, you probably find it most convenient to have the tax year be the calendar year and match up with your personal filing.

Many businesses have some concept of a "selling season" that makes it really convenient to not use January through December. A retailer, for example, probably prefers not to close their books on December 31 every year because of all the post-Christmas gift returns. Walmart has a January fiscal year (February 1 through Jan 31).

If you sold stuff to schools, you might choose a June fiscal year; most universities use a June fiscal year so an entire school year stays in a single fiscal year.

I have no idea why Apple chose September, but it was probably a rational decision.