AFAIK the two big services (BattlEye and EAC) both already support Proton.

Off the top of my head, the biggest games not supporting Proton due to anti-cheat are Destiny 2* and Halo Master Chief Collection, and Halo MCC is actively being worked on by Valve & Microsoft.

*despite running BattlEye now, the Destiny devs have a deep-seated trauma from their game being derailed by cheaters for the years prior before BattlEye, and thus make very obtuse choices like not allowing overlays or not flipping the BattlEye Proton switch and allowing Destiny 2 to run on Proton