I have never had much inclination towards writing in the margins of physical texts. While I have occasionally found annotations helpful to my understanding of some written works, adding them in myself feels like damaging the book. If I find something interesting or inspirational in a passage that I’m reading, I typically write it down somewhere else at length rather than adding my commentary into the pages of the book itself. I have not been required to annotate books in previous classes, though I have received assignments to make notes on photocopied pages, which I find less objectionable.
When reading a book, the thought never occurs to me to start making notes off in the margins, let alone dogearing pages; it seems unnecessary and disrespectful of the materials, and it’s perfectly easy to leave a bookmark in a place you want to return to later. This attitude may have risen from my habits earlier in life, which were quite different from those I have now; as a kid, I tended to be incautious with books, often writing or drawing in them, breaking the spine when opening them, eating on them, and carrying them around into places where they would be likely to get damaged. I ended up causing the premature deterioration of a lot of books that I would rather have intact today, and I still regret it. (I understand that not everyone who makes annotations is careless with books, I’m just explaining the formation of my own attitude towards treating books with care.)
Footnotes have proven useful to me in the past, though mainly in the case of books written in a foreign and/or archaic language. Notes made by translators and interpreters over the years are useful when trying to understand something written in a time and place very different from our own. However, in most cases these have been selected from a wider set of commentaries by the publisher as the most likely to enhance the reader’s comprehension of the text, and are formatted in a way that isn’t too distracting from the main text.
When reading a text to which annotations have been added by hand, one of the things that bothers me most is when text is frequently highlighted or underlined, which makes it difficult to read without noticing the annotations. While this might come in handy when attempting to abbreviate longer writings with a more informative tone, it is needlessly distracting in most other works.
Annotations to digital texts are a different matter. Many digital formats allow readers to make comments in a manner that is unobtrusive, but easy to view to those who are interested. They have the additional advantage of allowing for responses to people’s remarks, both for the writer of the original text (if they’re around to clarify) and for other commentators.
In conclusion, while I generally don’t go in for marginalia, I won’t discourage it as long as it is done in a way that doesn’t distract from the work itself.