There is a difference between being a monopoly and monopolist behaviour. One has successfully become the only one standing, one is seeking to shut out competition by one method or another. At least to my understanding.
The problem is that bundling is only considered problematic if your product is in a monopoly position. Bundling Internet Explorer was problematic for Windows because Windows was considered to have a monopoly in the OS market.
Apple has a pattern of purchasing companies that already offer products on other platforms and immediately shutting all non-iOS products down.
Obviously, they're free to run their business however they want, but it's also understandable that fans of those products might be upset that their app (or APIs that power other apps they enjoy) are no longer available simply because Apple did "their usual thing". Many companies (including Apple in rare cases) maintain or even develop codebases for applications across more than one platform.
There's nothing wrong with Apple buying companies to shut them down. It just sucks for the end-users who no longer get to use those companies' products for the sole reason of "they got bought by Apple".