Generalizations of the notion of "infinite sum" necessarily sacrifice some of the desirable algebraic properties of ordinary sums in order to attain greater generality. There's no "free lunch," so to speak.
The definition of "sum" under which the series you describe "sums" to $-\frac{1}{12}$ (clearly) does not have the property that a "sum" of positive numbers must be positive.
It's important to note that there's no "one true definition" of "sum," and that we may pick and choose which definition we are using for the purpose we're currently interested in. In some situations, it is useful to define "sum" such that Ramanujan's identity holds, even if it renders our notion of "sum" less ideal in other ways.