How old are you? I'll assume 16+.
Your parents have no right to say you can't take contraception, and they're being so very naive if they think stopping you taking contraception is in any way a good idea...
Firstly, good on you for being responsible.
My wife (started going out at 16) went on contraception without her parents knowing. There's a reason doctors aren't allowed to tell parents if you request it, it's none of their business. You are your own person and you are entitled to privacy and your own decisions. She's a very private person and didn't feel comfortable with her parents having anything to do with her contraception.
I also went to the doctors, even a hospital appointment without telling my parents at 15 for personal things - it's my body and my right to take it to the doctors and get treatment.
I'd say never budge on that issue. Especially given you were taking it for reasons other than sex! You have to suffer extra pain because you're parents whim? Hell no.
Regarding the secret keeping. What is their right to know you have a boyfriend? Similarly my wife kept me secret for a few months. Luckily there wasn't any awkwardness when she told them, because there shouldn't be. If they don't hold any ill-will towards your boyfriend and don't want you seeing him, why should you have to tell them? Just because?
It's your life. You can have what relationships you want, and they have no right to "know" who you are seeing if you don't want to tell them in my opinion. You don't say whether they have actually done anything because of it, sounds like there's just a bit of awkwardness in the air. That's probably going to happen even if you'd told them from the beginning, don't hold it against them. It's tough sometimes to see your kid grow up. You're at the age where you become independent from them, and they have to adapt to that as much as you, so the relationship might feel a bit strained - that's perfectly natural and not your fault, or theirs.
So don't feel guilty. You've done nothing wrong. If my daughter (in 15 years or so) had a boyfriend and didn't tell me I'd feel a little hurt, for feeling that she didn't perhaps trust me or we didn't have a relationship where she can tell me thing, but I know how awkward it can be and I don't think I could hold it against her or treat her differently for it.
I'm sure when you're 30 and have a new boyfriend you won't have to ring your mum to inform her straight away - but a few years ago you were a child, and your parents are probably still in that mind-set.
Time goes fast watching kids grow up, and sometimes they do it faster than you expect.