Holding a pen at a high angle is uncomfortable, that is a perfectly normal experience to have. That said, fineliners will perform best when held at a high angle, and while the tolerances will vary from brand to brand, getting used to holding your pen more upright is definitely beneficial - and more broadly, you should not be relying on how comfortable something feels to assess whether or not it is correct or not. There are lots of things that feel uncomfortable at first due to their unfamiliarity (for example, drawing using the whole arm from the shoulder), but which serve an important purpose, and for which that discomfort fades as familiarity and experience increases.