Parliament, especially the Torys in the House of Lords, was not keen to crown William as king. The only precedent for such a thing was Mary I and Phillip and that was considered to be a disaster (whether that is a totally historically accurate claim is irrelevant to the fact that at that point Mary's reputation was not good).

But William refused to be his wife's consort and it was his army that had sent James II fleeing. And Mary, herself, was a very pious woman who deferred to her husband. So, they ultimately had no choice to crown them both. And, beyond that, allow William to rule even after she died. She didn't rule alone because neither she nor her husband wished for that to be the case.

William spent a great deal of his time away in battle both in the British Isles (putting down Jacobites in Ireland and Scotland) and on the continent. So, Mary did handle a lot of the government administration in London when he was away. When he was present she let him control everything. She had little interest in asserting her own rule and preferred to be deferential to her husband. Despite that she could be a competent, decisive and efficient administrator in her own right when he wasn't present.