You're right in that the V1 and V2 didn't cause significant damage to the Allied side and didn't help the Germans win. But it still may not have been 'bad' for the Germans to invest in such weapons. The Allies would still have had to deploy their own resources to stop the attacks. (Every bomber sent to try to neutralize a V1/V2 launch site would have meant one less bomber available to attack a German factory/military target.)
Granted, it wouldn't have been enough to 'win the war', but it might not have been a total waste either.
Sure, there is that indirect effect, but it's a marginal one at best considering the resources Germany devoted to those two programs.
By September 1944 the Allies had such a vast air force at their disposal that any diversion would not have significantly affected its striking power. At that time, between the 8th and 15th air forces, there was a total of about 3,000 heavy bombers plus nearly 1,000 fighters available for operations. Bomber Command contributed another 1,300-1,400 heavy bombers. Then there were the Allied tactical air forces, which added about 1,000 medium bombers and 3,100 fighter-bombers to the sum.
This was the aerial armada Germany was up against. (Then to that we'd have to add the Russian air forces.)
(Historical footnote: the majority of attacks on V-1 sites were undertaken by Bomber Command. The USAAF only conducted such attacks when otherwise unable to operate against German industry. In July and August of 1944, for example, just over one-quarter of all V-1 site raids were performed by the USAAF; the remaining three-quarters were by Bomber Command.)
They certainly had the men to pilot those Me-109s - though actually I would suggest building FW-190s. And pilot training is just one more use for resources. So instead of building 1000 planes with no pilots, maybe they could have cranked out another 800 or so planes with capable pilots. Or they could have expaned the pilot training program so that all the planes they already were building got decent pilots rather than half-trained rookies.
The problem for pilot training wasn't a lack of aircraft or trainees, it was a crippling lack of aviation fuel—there simply wasn't the fuel to spare for training flights. And in-flight training is crucial in producing a good pilot who knows how to get the most out of his aircraft. In May of 1944, German production of aviation fuel came to 156,000 tonnes; in September, production had fallen to just 10,000 tonnes. This compared to the 320,000 tonnes per month the Luftwaffe actually needed. When the fuel begins to run low, the first thing cut are the training missions so that the fuel is there for the combat missions.
It didn't help that German policy was for its fighter pilots to fly until either killed or rendered too injured to fly. In contrast, the U.S. sent its fighter pilots home after one or two tours to help train the new recruits, and the combat experience provided by such veterans was invaluable.
