Question: As far as i have understood it, Photons do not have Charge. Charge as i have understood it is the Positive and Negative charge of an atom.

In context to $\rm H\_2O$ being a polar molecule, microwaves ovens utilise the positive and negative polarity of the microwave to agitate the $\rm H\_2O$ Molecules creating kinetic energy and heat.

How is it so, that an EM Wave that has no charge, is able to agitate the charged particles of $\rm H\_2O$?

Answer: 
The charge of individual photons is indeed zero, but light, or microwaves, contain *oscillating electric (and magnetic) fields*.
Charged particles and electrically polarized molecules such as $\rm H\_2O$ will experience forces when they experience these electric fields.

When the microwave oven is turned on, and the microwaves pass through the water,
the polar molecules of the water will constantly try to align in the appropriate direction (one that minimizes energy) with these electric fields by constantly changing their orientation inside the water (as the direction of the electric field keeps flipping).

As these molecules continually change orientation *extremely quickly* (millions of times per second), this vibrational motion causes the water molecules to gain kinetic energy which increases the temperature of the water.
Photons has zero charge, but they still can interact with electricity. They can participate in kindof "chemical" reactions with charged particles, including electrons.

Actually photon is a carrier of electromagnetism, it is "main" particle of it.

The energy of photon is $h\nu$, where $\nu$ is it's frequency. For microwaves from the oven, this formula gives very tiny value. This means, that oven's microwaves consist of a "sea" of brazillions of very tiny photons. These photons don't act individually, they act collectively. The collective action of such photons can apply some electric force on water molecule and make it rotate.