In a Transformer - Alternating current flows in primary winding
Yes, but how much flows? See later.
Causing alternating magnetic field in Iron core
Yes, but that's not the entire current-causing-flux story, see later
Which causes alternating voltage in secondary coil.
But I am confused that what would be the polarity of the Flux caused by the secondary winding voltage.
The secondary winding voltage does not cause a flux. The only thing the secondary winding voltage might do is push a secondary current through an external load. That secondary current will generate a flux.
Won't the Flux caused by the secondary voltage cancel the Flux caused by the primary voltage and thus making the net Flux zero in the coil if both the primary and secondary windings have the same number of turns?
One way to look at it is that the flux caused by the secondary winding current cancels some of the flux caused by the primary current, leaving a residual flux that magnetises the core, and whose changes generate the primary and secondary voltage.
Another way to look at it is that the net magnetising flux in the core has to generate the primary voltage. As the primary voltage is constant, the amplitude of the magnetising flux in the core has to stay constant.
When the secondary is open circuit, the primary current equals the magnetising current and creates the core flux. When the secondary gets loaded, a secondary current flows, which would decrease the core flux, were it not for the fact that the primary current increases to cancel out the secondary current, leaving a difference between the primary and secondary fluxes that is the magnetising flux.
In a good transformer, the magnetising current required might only be a few percent of the full load currents to generate the magnetising flux. In an ideal transformer, the magnetising flux is still finite, but the magnetising current is zero, because the ideal transformer has an infinite permeability core (or approaches zero as the permeability approaches infinity)