This song means " All the good things in life you have to suffer.. but for a little..then there you go"... every one has to suffer but in the end there's something to be good for you.

This song seems to be about the self inflicted pain that humanity feels in our day to day lives. We all feel the pain, yet we're blind to it and do nothing to end it.

The part "An unturned stone, an undiscovered / door leading to the gift of hope renewed, eternity for you" refers to our desperate pleas for science to cure all our problems and end our suffering.

The ending of the song: "The masses of humanity, still clinging to their dignity, / the masses of humanity will always have to suffer" refers to our belief in humanity being the epitome of creation and us refusing to think otherwise. Our disregard for nature and for different cultures/ races is what causes our suffering. In believing that we have a higher purpose/right to exist then these other people we create the problems that plague our world and will continue the cycle of suffering and pain.

When, in the song 'Suffer', Greg sings "an unturned stone, an undiscovered door" in the chorus, he is referencing a novel written by Thomas Wolfe, first published in 1929, called "Look Homeward, Angel". The very first words of the novel are "[...] a stone, a leaf, an unfound door; of a stone, a leaf, a door. And of all the forgotten faces."
At the very end of the novel, within the last twenty pages, he speaks of the unturned stone and the unfound (or undiscovered) door.

This song is obviously about how mankind has always had to and always will have to suffer but it is due to our own faults; we always will have to suffer but have no one to blame but ourselves.