The offical reasons were speed and security, which was obviously a farce since all the major browser vendors wrote their own PDF viewers which is both slow and known for tons of security issues as well.
They could have just as easily wrote their own fast and secure implementations of flash and Java instead of disabling them. Especially for Java given Google's deep experience with it and that they already have their own runtime.
Apple may have fired first on flash but google recently disabled all NPAPI plugins in chrome as well. The reason... "Security". I guess code not made by Google isn't secure enough to be used on the internet?