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There seems to be a widespread misapprehension that "free" tools are worse or amateurish. In fact, these days, in general, the reverse is true. Commercial software is generally geared towards the ignorant, try to be everything to everyone (thus bloat), and are often defective by design in ways that make the user have to pay more money if they want even mundane "extra" features, or prevent them from learning things that might help them be less dependent on them in the future, and/or prevent their software from working on conjunction with software not made by them.
Firefox and Chrome are open source and better in most ways than their commercial counterparts, IE and Safari. Apache and WordPress are free software, yet there is nothing even close in quality in the commercial world. The list goes on.
But the worry about the ePub format, and thus the tools for it, not being very mature is a more reasonable complaint. There's some truth to that. However, from what I've seen calibre and Sigil produce ePubs that are at least as high quality as the ones produced by, e.g., InDesign. Perhaps that would change. But for the moment, the only argument I could see for preferring InDesign would be if you were already using it typeset the print version of the book. (And in general, I think it's overrated; I think TeX's typography is at least as good, and it's free.)
But also keep in mind that ePub is somewhat different than most "new" technologies, since it's built around pre-existing technologies: XHTML files with XML metadata wrapped up in a .zip file. There are open source tools for all those pieces that are old (many older than their commercial counterparts), stable and very well-tested.
That said, I still think the best way to produce an ePub is to edit the XHTML and XML pieces in a text editor and then zip them up, rather than using any specialized software.
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