There are at least 4 FREE apps which do the same thing (my favorite is remux). Though none of the free alternatives can convert FLAC streams in a movie file (at least not that I know of), I have NEVER, EVER seen a FLAC audio stream in a movie file (and I work with multiple formats from various sources every day).
But, even if I were to find a FLAC stream in a movie file, there are several free tools that can be used to quickly and easily demux the stream (I like MKVTool), convert the audio independently to AC-3, AAC or whatever (my favorite is XLD), then remux it with the video stream into an MP4 file (I like Subler). Though some apps will only mux/remux to the .mp4 extension, if you simply must have the .m4v extension for iTunes compatibility (which, IMHO, is a horrific way to watch media, so I never use it), just change the .mp4 extension manually to .m4v (because the only difference between them is that Apple made the stupid decision years ago to force its native apps (like iTunes) use a proprietary extension.