Solutions to the Klein-Gordon equation can be interpreted as wave functions or operator fields.
Interpreting solutions as wave functions leads to relativistic quantum mechanics (RQM). This has all the nasty negative probabilities you've heard of. RQM is rarely taught in classes; people who need it learn it.
Interpreting solutions as an operator field, however, leads to one of the useful quantum field theories (QFT), namely spin-zero field theory or scalar field theory, or whatever else it's called. This theory has positive probabilities & energies. Yay.
A particularly straightforward way to derive spin-zero QFT is to start with the RQM solutions to the Klein-Gordon equation. Then, you just simply re-interpret the solutions as an operator-valued field, and impose particular commutation relations between the operators. Bam, QFT.
Source: Chapter 3 of Student Friendly Quantum Field Theory by R. Klauber, some of which is available free online here.