Although the spec is huge, there is plenty of sample code online to get it working. You do actually have to read it though to understand slabs, hyperslabs, strides etc. Once you get though, its really versitle.
As far as speed, we used it to replace our propriatary data format. We would have to provide readers to all the scientists that use our data. It was nightmare. Some people want stuff in R, some in Python 2.7, some in Python 3.4, some in Matlab, and the list goes on. HDF5 gets rid of all this.
When in the field and the system shits the bed, its really easy to open an HDF5 file in HDFview and inspect the file contents. I dont always have matlab available when im in the field, same with python. Sometimes I just need to look at a time series and I can diagnose the problems with the system.
For me, its silly in 2016 to have any kind of proprietary binary format when something HDF5 exists.
Many of the complaints the author had makes me think he the stereotypical scientist of really smart in one area but cant program worth the beans. I dont think that HDF5's fault.