Can I buy an iPhone 6 from the Apple Store and put my own SIM card in?

I'm with rogers and have the iPhone 5C. I'm planning on buy an iPhones 6s from the Apple Store, so would I be apple to put my current rogers SIM card into that one?

Yes. Apple only sells the phone, in any case, so you'd be responsible for providing a SIM on a new phone from the Apple Store. If you have the SIM with you, they'll install it, although you can also do that on your own.

At the Apple Store, they'll probably also help you to install the correct APN settings for Rogers (in order for you to access Rogers' server for wireless internet). This, too, can be done on your own. (unlockit.co.nz)

As long as the phone is compatible and unlocked to work with your carrier's network, yes.

Usually Apple when buying through an Apple Store would give you the option of setting it up for a specific carrier or unlocked, either way it should work out.