Don't get too hung up on the notion of "negative" here. The sign is arbitrary. When electricity was first discovered to flow, they decided to call one side "negative" and the other side "positive". In fact, they guessed wrong: it's actually the electrons flowing (at least, in direct current), and they flow from the negative terminal to the positive. It doesn't really matter. The sign is arbitrary.
So electrons aren't "negative in nature", in the sense that they don't exist or negatively-exist or something. They do exist, and they do have charge; it's one of the fundamental properties of electrons. That charge is in a certain amount, and it just happens to be the exact opposite of the amount of the charge on a proton. We could multiply both values by -1 and get precisely the same physics. (I'm glossing over a bunch of caveats there, but that's the gist.)
Exactly where that charge comes from is really hard to say. Right now all that can be meaningfully said (in the context of a question like this) is that it's one of the fundamental properties of the universe.
