I am a PhD student – I read a lot of academic articles and the occasional academic book. I have an iPad. I don’t print anything. I have a system in place that helps me keep all my reading organized. I believe that I am a pretty typical representative of the future of academics.
Nothing frustrates me more than when you provide an article in electronic format (PDF) and then disable the ability to annotate that article. You pretty much make your article useless to me – as you make it significantly more difficult for me to take notes and cite your publication. Note that if you don’t provide your article in electronic format, I won’t read it at all.
Now, if you are a publisher of books, you too need to think of about the needs of your audience. An eBook that doesn’t let me annotate is useless to me. If I can’t highlight important quotes and sections, and copy those quotes then your eBook is of no use to me.
So, for me, as an apprenticing academic, who is also looking to publish, I will take into consideration the usefulness of your product before I submit my article/book chapter. If you are closed-access, I will think twice before submitting. If you do such foolish things as “protecting” your documents from annotations, I will choose to publish elsewhere. By “protecting” your content, you are severely reducing the impact of the content, and frankly, you are annoying the hell out of me!