Well, there could be several reasons. For one, if it were an array, you could modify it. You can't modify a FileList instance. Secondly but related, it could be (probably is) a view onto a browser data structure, so a minimal set of capabilities makes it easier for implementations to provide it.
You can convert it to an array via a = Array.from(theFileList) (that's an ES2015 method, but it's trivial to polyfill it) or via a = Array.prototype.slice.call(theFileList).
Update in 2018: Interestingly, though, the spec has a note on FileList:
The FileList interface should be considered "at risk" since the general trend on the Web Platform is to replace such interfaces with the Array platform object in ECMAScript [ECMA-262]. In particular, this means syntax of the sort filelist.item(0) is at risk; most other programmatic use of FileList is unlikely to be affected by the eventual migration to an Array type.
I find that note odd. I thought the trend was toward iterable, not Array — such as the update to NodeList marking it iterable for compatibility with spread syntax, for-of, and forEach.