To the original poster...
Ignore these assholes.
The backing recording was likely recorded in a more ideal environment than you have. Don't feel bad, many of us suffer that common circumstance, we don't have an ideal recording space. To help remedy the situation it would probably help by trying to eliminate your room from the recording as much as possible....less room, more flute. How we do this is by close micing our instruments. After you get a nice clean performance from your flute you can then experiment with placing the flute in a virtual space using effects, such as reverb. Having eliminated your space from the recording is important because you would not want any conflict between your space and the virtual space in which you eventually place your flute. That is why it is important to record a nice clean and dry performance on your flute, it then allows you the opportunity to experiment with reverb and such to find the right fit to blend into the room in which the backing track was recorded.
Take care with the reverb, a little can go a long way. A common practice is to tweak up the reverb until you can hear and notice it, then back it off from that point a bit. Although, flute can sometimes benefit from a fair amount of reverb. It's really up to you, experiment, keeping in mind that your goal is to blend in with your backing track.....which is often achieved by making it sound as if
all tracks were seemingly recorded in the same space/environment.
Good luck and have fun, you'll do fine. Post up some samples, i'm sure some of these assholes will be more than happy to tell you where you are going wrong.