I think you may be misinterpreting the purpose of a compliment a little.
Typically, people give compliments because they want to make the other person feel good about themselves (I often give compliments I know aren't strictly accurate because I know hearing it would make the other person happy). You said in a comment, "I just feel like I didn't earn the compliment, so I don't feel comfortable with it", but lets look at an example.
If someone says "good job on making that website", I don't think they're necessarily saying:
"this is an objectively impressive thing you've done"
"I want you to know I think you've done something impressive."
Which is (I think) a subtle but pretty big difference.
It's true that you could argue you haven't done something impressive. However, you can't argue that they shouldn't want to tell you that you have. That part is objectively true, and honestly, if you responded with "you shouldn't want to tell me that", that might be a little rude.
In that sense, it's hard to say you didn't "earn" a compliment, because compliments aren't strictly attached to merit. In a weird way, if someone gives you a compliment, that means you've already earned it; you've already done something that makes that person want you to feel good about yourself.
All in all, I think it's ok to deny that your accomplishment is as impressive as they're saying. However, this can't be done by denying that you "deserve" a compliment at all, and it can't be done too often. It's important to be mindful of why this person is giving you a compliment. Most of the time, you'll find it isn't to make an objective fact about you. Rather, it's to make you feel good about yourself, and usually getting mired down in whether or not you've done something "worthy" of feeling good is missing the point.