I too find the rubber cover annoying ,but , the problem is that the retention clips tend to break often and the cable boots are good option to prevent it from happening.Once the retention clip breaks off the cables , they tend to slide off the router / modem / switches and make the network unreliable.
My Experience :
I bought two cables a few months ago : One with cable boot (red) and the other (black) without.I mess around with the cables quite a lot and here is a picture of the two I taken for the purpose of illustration when I saw this question:

My point is that the one with cable boots tend to break less often.

Once , the retention clips breaks off , when we plug in the cable to ports they never clicks and they fells off from the port easily.
I personally find the cables with cable boots annoying but on the long run they prove to be useful.I will discourage you from
cutting off them since they are useful .But , if you are skeptical and annoyed about the existence of them , you may cut off them since they do not pose any threat to the connection itself.(If you plug the cable in the port and forgets about it , the cable boots may not be of much concern : You surely can break them apart)
It is not clear whether cutting of the plastic cap affects performance of the cable, detailed measurements of bandwidth transfer rate and stress testing is required to settle it conclusively.
@user77469, What‽ ಠ_ఠ