I think it depends on how you choose to look at it… Find the good out of everything you know?
So I can’t say much on the playing of the flute, since I don’t play flute… but the fingerings for that and whistle are pretty much the same all around.
Pipes, ah the pipes. Aren’t they calling? Well, I’ve only been piping about 10 months, so by no means have I mastered this instrument. However, I have been told how rapid a progress I am making by a few different people, and honestly to which I can only give credit to having spent a very solid 3 years playing tin whistle before ever touching a pipe chanter. Even more proof that the fingering between whistle and UP’s are similar… Well when I first started piping, I bought a practice set, that was, well, set up for the more common right handed player, ie, bag under left arm, left hand on top, bellows under right arm, right hand on bottom, chanter on the right knee etc… Well I bought the set as it was, and gave a good go for about 2 months. During those 2 grueling months, I was barely getting anywhere, and mainly it was the fingering that was throwing me off. I tried transferring simple tunes I had already knew on the whistle, onto the chanter, because I figure the fingerings are the same, so it should be no prob. Well those simple tunes I had already known, felt very alien to me all of sudden, as though I had never knew them in my life. I mean even learning the simple scale of the chanter was proving difficult, and yeah I learned one or two simple tunes, and if I thought real hard, I could play some tunes I didn’t normally play right handed, but this wasn’t working, and it was confusing the hell out of my brain… The thing was, I play whistle LEFThanded, left hand on bottom, right hand on top… I brought this up with my teacher, and he suggested that I switch the bag and bellows around so that I have a LEFT handed pipe set. So I had to start over with re-learning bag and bellow techinque (which was very weird immediately after the switch…) but I did, and before I knew it, tunes on the chanter started coming to me, simple ones of course, nothing fancy like the Bucks of Oranmore but never the less, and that familiarity came back, and I’m feeling a lot more comfortable now playing the pipes the “way” I do whistle, and I’m only certain that it’s from having a good grasp on playing the tin whistle before ever jumping on the chanter. I don’t think it could be anything else.
Now obviously pipes and whistle fingerings are similar, so don’t get any ideas that tin whistle playing is going to make you a great piper, among other aspects in piping, you can’t practice staccato fingering on the tin whistle.. My point was that learning the tin whistle, and spending a great deal of time on it before ever playing pipes, has really been a help for me learning the pipes.
(My reasons for trying the pipes right handed at the start, were as I soon discovered anyways, just rediculous, so I won’t even mention why. Live and learn anyways…)
The only other thing I could think of where flute playing might help your piping, is for phrasing. Good flute players seem to really know how to phrase for obvious reasons.
So my long, boring point is, the tin whistle is quite the handy little instrument as far as I’m concerned, and can help you down the road should you decide to take up flute, or pipes, or even whistle! 
Best of luck where ever your journey takes you,