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Whilst obtaining an approved I-129 application is a require step for many US work visas, it is not in itself visa application in any sense of the word.
Without your I-129 being approved, you would have never progressed to the stage of actually applying for a visa (ie, filling out DS-160 and attending an interview at a US Consulate), and thus you were never refused a visa - as you never applied for one. Thus you can safely answer "NO" for this question.
The I-129 is a form filled in by the potential employer to obtain permission to employee a foreign worker. That's very different to a visa application which would be submitted by the individual requesting permission to travel to the US.