Because the captain liked Hobbs and didn't like or trust Wellard. It's the same reason he let Randall off after the beating he gave to Styles; he had his favorites and made no bones about it.
Further, as the gunner, Hobbs is a warrant officer in his own right, the same rank as the sailing master, purser, bosun, surgeon, and carpenter. As such, he cannot be disciplined in the same way a regular seaman can be; he cannot be flogged, for example. His status relative to Wellard is nominally inferior, but in fact they are really much more equal; it's expected for the young midshipmen to learn from the gunner, just as they do from the master and bosun.
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