Yep,
RAF Lodge dates from the First World War (as indeed do many military Lodges). The Lodge meets in London 4 times a year (I think). As with all Masonic Lodges the majority of members will be retired (you can be a Mason for your whole life), but there will be a number of serving members.
There is also a RAF (Warwickshire) Lodge which is peripatetic and meets in Masonic Halls close to RAF bases. Until recently (when a ban on meeting on military bases came into force) this Lodge used to then visit the nearby base. Most members are ex-RAF from days of yore. My friend Flt Lt Jim Pearson-Smith DFC, former President of 101 Sqn Association, was a Past Master of that Lodge (he was crew on an aircraft that sank the Tirpitz).
When I was at Brize the Master of the RAF Lodge was a member of 10 Sqn. There were at least 7 Masons amongst the Operations Wing staff at that time.
My own Lodge currently has a retired V-Force Sqn Ldr as Master. When I joined we were dominated by Engineers and it almost became a gathering of ex-Halton Apprentices ranked between Sqn Ldr and Gp Capt.
I know of a couple of AVMs who are Masons and I suspect there are more.
I don't believe for one moment that Masonic membership harms the service, and those who know me will note that I never gained any priviliges within the service as a result of my membership.
Hope this helps.