Like its opposite male- (bad), bene- (good, well) is simply a Latin adverb used to modify the meaning of words. A benediction is a ‘good speaking’, particularly a blessing in church. A benefactor is a ‘do-gooder’, though without negative connotations; it is most often used to mean a ‘patron’. The person who receives the benevolence of a benefactor is a beneficiary. People who inherit are beneficiaries of a will. Beneficial means ‘doing good’, in the way that fresh air benefits your health.
A related form, benign-, meant originally ‘well-born’ or ‘noble’. It now turns up in words meaning ‘kind, friendly’, such as benign and benignant. You can compare the change in meaning of the word gentle, which also started off meaning ‘noble’, as in gentleman and of gentle birth.
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