If you don't mind a little bit of constructive criticism, I see two things wrong with your message (assuming your messages aren't much longer than the one you mentioned originally).
msbxa said:
All I said was something like this:
Its nice to see someone with similar interests to me in fitness and nutrition.
You look great! You must get a lot of messages and attention.
How could I stand out among all competition? Well, I may not have much, but I am a genuine, gentle, honest, respectful person. Something that I think is rare.
Then I asked a couple of harmless questions from her profile.
The bolded part is a problem for two reasons - one, "I may not have much" seems like you either lack confidence in what you do have, or that you really don't have much to offer (in which case you aren't going to stand out from the competition). Either way, I would leave that off. Also, when you say "I am genuine, gentle, etc." - although it is true that these are rare qualities, they don't really say anything about you because she doesn't know if they are true since anyone can say those things about themselves (again, it doesn't help you stand out from the competition).
Also, the line "You look great! You must get a lot of messages and attention." doesn't help you stand out from the crowd at all - if she's that good looking, she probably hears that from a lot of the guys that message her.
Asking questions relevant to her profile is good - and mentioning common interests at the outset is good; but to be honest with you, I would be more specific with that. I would also use the subject line with something eyecatching (using a statement with ellipses sometimes works), so it would be something like:
Subject: I couldn't help but notice...
Message: ...that you're a fitness buff like me. Have you ever run a 10k? I just ran my first one a few weeks ago, and thought it was exhilarating. I plan to do another one soon.
I also noticed that you're into [something that she mentions in her profile]. What got you into that?
Talk to you soon,
MSBXA
Having said all that, sometimes women just aren't interested for whatever reason - but I have had success at getting return messages from that kind of format.
Hope that helps.
One other thing, I usually try to be playful in the message (but that's just me) - something like (and this is a real example) "I have to ask...what in the world were you doing wearing a coat in a nightclub? If there's one place you never need a coat it's in a club." (based on a picture she had on her profile) - it isn't really teasing her, but it's a little bit of lightheartedness, so the message doesn't seem like an interview.