Age 2.5? My advice would be to continue with toddler-type fun classes.
She really is too young to handle a flute -- most orchestral wind instruments aren't started until at LEAST age 8 or so, often even older. They need the muscle strength, hand size, finger independence, and breath control, that doesn't come until they're much older.
I don't know anything about that preschool flute, but it might be a fun option for her. There would be no problem down the line changing to a "normal" flute. They are so different that it would be learning a new instrument -- possibly with a carry-over of a similar embouchure. It would be no different than a young kid learning the recorder then learning the flute later, or learning the ukelele then moving later to guitar, or playing a toy or an Orff xylophone and later learning piano. There will be some skills carried over, but there is absolutely no detriment or confusion or anything.
"Suzuki" is technically a method of instrument instruction and while it is most commonly associated with string instruments, it is applicable to anything. However, you're right in that it will be fairly difficult to find Suzuki teachers for anything other than strings and piano. Of course, part of that could very well be because most other instruments can't be started with preschoolers.
Is the flute something she has expressed interest in, or is it your leaning because you play it a bit yourself? At just 2.5, she probably hasn't been exposed yet to the full range of instruments. I honestly think the best approach would be to keep her in general music classes -- look into things like Kindermusik and Music for Young Children as well as whatever else you can find -- and take her to concerts (many orchestras have concerts geared to young kids), rent videos of Peter and the Wolf or the Young Person's Guide to the Orchestra, fun concert things like that... find some books about music and instruments... and wait for her to express an interest in something.
"Oooh mommy I want to play the TROMBONE!!!" she might say.
Or if she likes the violin, she could start that right away. Maybe she just wants to keep singing -- join a choir. She might choose the piano -- best to wait til age 5 or 6 unless you find a teacher who *specializes* in preschool piano.
But in the meantime, it's more important to just let her explore music in a fun way rather than worry about "learning an instrument" just yet. Have some good-quality "toy" instruments at home to play with -- maracas, a tambourine, a good xylophone, a slide whistle, things like that.
When I was that age, I just had my Fisher-Price xylophone. I can actually *remember* trying to pick out "Doh a deer" on it. I'm not even sure where I learned the song, whether mom had sung it to me or if I'd seen the Sound of Music... But I distinctly remember figuring it out, one note at a time, over the course of days or weeks, recalling what I'd already figured out and trying to add the next bit... And my mom says I was only 2, not older than 3 when I did that.
My first music classes were the regular school classes when I was 6. My only exposure to the piano was goofing around on one when we'd visit my grandmother. At age 8, I finally started piano lessons. I now have a Master's degree in piano and I am a professional musician.
The moral of that? Don't worry about starting lessons NOW, there's lots of time.
If she's keen on something, by all means follow up on it! But don't fret if you can't find something appropriate for her age or if you have to wait a few years before she can start her "favourite" instrument.
Just let her explore and enjoy music and see where it leads!