I DEFINITELY KNOW THE FEELING. I got the idea for a story where a main character is a glitch in a video game and started fleshing the whole thing out literally two days before seeing Wreck-it-Ralph in theatres. I spent the entire movie just screaming internally, but then went home and kept working on my story idea! xD As I developed it, I realised that the similarities are pretty superficial.
I really don't like idolising the concept of a "unique" idea (as everyone above has already said, there aren't really any unique ideas) -- but even if you had an idea that literally nobody has ever had before, that won't actually make your story better! If the characters are extremely believable, or the story told extremely well, those are the kinds of things that make a story Stand Out as something special!
For me, ideas become something special as they develop. On the surface, everything sounds cliche, because cliches are just ideas that remain shallow. If you shoot down every idea that's "been done" before, you'll never get to the point of finding what makes your story cool and special.
And if someone points out to me, "Wow, this video game story is really similar to .hack//sign!" I can either respond "oh no, is it??? Aw shoot now I look like I'm copying but I promise I never saw dot hack >A<;;;;;;; I gotta figure out how to change something ;;" or I can respond "lol really? That's cool, GREAT MINDS THINK ALIKE" and keep going forward. The way you look at it will definitely affect the way your readers approach it -- if you are not defensive and okay with the idea of things existing that look kinda like your thing, chances are your readers will be too!