In the poem, people are throwing stones at the patriot and wants his death apparently because of some misdeeds he has done in the last one year. But from the tone and the language used by the speaker, especially towards the end of the monologue where he keeps faith in God and hopes to be repaid by the God, it seems that he is actually innocent and his good works have been misunderstood by the masses. It might be so that he is guilty of some things he did which he thought were right.
 
The patriot might have taken some tough decisions in the government for the long-term benefits of the people but it caused difficulties in the short term. He might have made some stricter rules for the good of the country but people misunderstood it. He might have made some wise movement in the right direction but it was against the public sentiment. Anyway, we cannot be sure about what his misdeeds were, but that was something he thought right, but the masses thought wrong.