The Quest 2 has minimal inter-pupillary distance (IPD) adjustment — only three fixed options. If your eyes don’t match closely enough to one of them, it can be very uncomfortable. Mine don’t, and I have the same experience as you, but I can put up with it for short bursts. More expensive headsets have much better lenses and adjustment options. It’s not an inherent problem with VR, just concessions to make a cheap device.