Please, Microsoft, do this. An iTunes designed for Windows would take 90% of the irritation I have with my iPod away (and would just be a generally classy move on Apple's part—providing the best experience of their hardware, regardless of your choice of OS.)
I'm a huge Linux and Open Source fan, but my iPod Touch is the best portable music player I've ever owned. I'd say 50-75% of my coworkers use iPhones as their music players too. And we're not all college kids or fanboys.
Why would you put FLACs on a portable device without transcoding them first? Do you have TBs of room on your player? (My collection is currently 300GB of average-quality MP3s, and growing...)
Crappy earbuds are more likely to expose flaws in lossy encodes than high-end gear.
The psychoacoustic model assumes that certain sounds will mask other sounds so you can leave them out or replace them with something that doesn't sound quite right. If like most cheap headphones you don't have a flat response then the masking sound can be too low to work as intended.
Having said that, with modern encoders it's mostly not an issue, even if you're using 90kps Vorbis created specifically for portable use. What is an issue is that you'll probably want to use the same file for portable and home listening, or you'll have got the file from someone who wanted to be on the safe side, since some songs are trickier to encode than others, so you'll end up with a 256kbps AAC file from iTunes, or 320kbps MP3. At that point the jump to FLAC compression sizes isn't particularly great and the management becomes a bigger hassle plus it allows you to transcode to various other formats and sizes as required, saving even greater space for listening in noisy environments like cars, trains, buses etc.
FLACs use less battery than lossy codecs (at least on flash based devices, since the extra reads don't cause a disk to spin up). It's a tradeoff of course, but if you've got the space (and this is only going to increase) and don't need instant access to a giant music collection then it's worth considering, particularly if it lets you skip a transcode step.