The force law $F=\frac{Gm_1m_2}{r^2}$ holds, in general, only for two point masses. As it happens, if a body is spherically symmetric and you're strictly outside that body, then as regards the gravitational force it exerts (though not necessarily the force it experiences), it can be replaced by a point mass (of the same mass) at its centre.
In particular, if your mass is $m$ then the Earth's mass $M$ exerts a gravitational force $F=\frac{GMm}{r^2}$ on you, as long as you're not underground, where $r$ is the distance between you and the centre of the Earth: in particular, $r$ is at least as long as the Earth's radius $R=6300\:\mathrm{km}$, a long way from zero.
If you do want to go underground, then the force you experience changes. In particular, it turns out that the gravitational attraction from the spherical shells of rock above you precisely cancel out (because some bits point one way and others point the other way), and you're only attracted by the volume of rock underneath you, which scales down as $r^3$. The upshot is that the gravitational force underground goes roughly linearly with the distance $r$ to the centre of the Earth, $F=\frac{GMm}{R^3}r$ (assuming constant density!), and there is no singularity at the centre.
If you do have point masses, on the other hand, then the force law $F=\frac{Gm_1m_2}{r^2}$ does hold, and at $r=0$ there is indeed a singularity, and there's no getting around that. This causes all sorts of headaches, particularly in electromagnetism (where the Coulomb attraction is identical, and where we needed to invent renormalization to deal with the singularities) but in many ways these are only present on the theory side.
Unless, of course, you've got a pair of true point masses in your desk drawer, in which case you've got a promising future in physics ahead of you.