I'm no technoguru but I thought it was to minimise the airspace in the reservoir,it wont improve anything getting rid of it,so I'd keep it. Its the same for the brakes too.
it somtimes gets a bit out of shape as the fluid goes down, take it out and put it back in shape, bleed your brakes while your at it, top up with fuid to the upper marker whip it all back together and the job is job'd
I was always under the impression that clutch/brake fluid is susceptible to contamination from humidity and air (both water & air compress a lot more easily than hydraulic fluid) so the rubber minimises the amount of air that the fluid comes into contact with.
As always, I reserve the right to be completely wrong.
It is also the seal that keeps the fluid in and the air/moisture out. Leave it where it is if you want your clutch fluid and pistons/seals/cylinders to stay in good nick. It is collapsible and should be pressed flat into the cap when fitting after topping up the reservoir. There are similar ones in the brake reservoirs.