Anecdotally, users seem to trust native button more. If it looks like you made your own PNG and linked it to Facebook, they can't trust that you aren't going to try to do something shady to their Facebook account (or open a popup). If you use Facebook's button, it's a familiar experience without providing the publisher's site the opportunity to play man-in-the-middle.
User perception matters. Facebook's button seems to be perceived as more user-friendly than the unknown button on someone else's site, even if the unfamiliar button was designed to be less hostile than Like.