This version was released last year. At that time, transparency support was experimental and not part of official library/binary. So, what you are seeing here is an image with stripped alpha channel.
The good news is that the next version of WebP library/binary (v0.1.99) will be release very soon (in a week or so). This will add both transparency and lossless compression support.
Meanwhile, if you want to try out transparency/lossless support, I'll encourage you to compile cwebp & dwebp tools from the latest source in Git repo:
To get the source:
Compilation:
cd libwebp
./autogen.sh
./configure
make
This will create cwebp & dwebp binaries under directory examples/.
Also, try out the new "-lossless" option in cwebp.
Let me know how it works for your image!
Thanks,
Urvang