There's nothing intrinsically wrong with Indesign. It is still one of the main programs people use to create books (printed or digital) throughout the world, and if your clients demand p-books and other printed materials, you just can't afford to ignore it. Also, you can do a lot of e-production with it, like iPad/Android apps, fluid and fixed layout ePUBs, and even kindle books – though I don't particularly recommend doing Kindle files within Indesign. If you plan to work as an independent eBook professional, it's an important, yet expensive, tool to master.
But, at the same time, I wouldn't say that it's the best option for ePUB and Kindle formats, not at all... It has advanced a lot in recent versions, but still have a lot of room for improvement. At least for this two particular formats, you should really be intimate with markup languages (HTML, CSS), eBook specs, source code editors, and even programming... This will save a lot of time and headaches later on, and will strengthen your knowlegde of the digital publishing as a hole.