Whether to use a screen protector or not seems like a very personal decision, based on opinions I've read on XDA. But I recommend using one. The Flyer does not have Gorilla Glass, and several people on here have had problems with scratches. The difference in feel is pretty minimal with a good quality protector, even when using the pen. So I don't think it will bother you in this regard. Some people even like the feel of the pen with the protector better than without. Apparently, the matte protectors (which I don't have) provide a little more friction, so the pen slips less and feels a bit more like writing on paper.
I have a Skinomi protector, and happy with it. I've also used Bodyguardz on my phone, and very happy with it, as well. But at the time I bought my Flyer, Bodyguardz didn't make a screen protector for it yet. But now they do.
If you end up not liking the protector, you can always take it off. Then you are just out $15-20. Better than going without, and regretting it, as there is no easy way to remove the scratches once they are there.
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Phone: HTC One X (AT&T version) Rooted, Bootloader Unlocked, S-Off
Tablet: Samsung Galaxy Note 8 (WiFi only) Rooted