A condom facilitates many social evils which all religions condemn, besides providing protection against STDs. As a religious icon the pope had to weight the pros and cons. His logic could be this:
No condom --> Fear of STDs may prevent illegal sex and hence STDs and in the long run may actually throw away the real evil(AIDS)

I read at several places that a condom may not prevent the conception itself then how can it prevent STDs.

Those who think sex should be free like food ofcourse cann't afford to giveup condom anyway...