Short answer is that Louis was the main target as the living embodiment of the French monarchy, and at that time it was a huge deal to kill a monarch for being a monarch, even for hardcore republicans, so they focused on him first, before turning to Marie Antoinette when they had accomplished their goal and set a precedent.

Contrary to popular belief the revolutionaries actually stuck to a rather complex legal procedure before executing Louis XVI, it was not done on a whim or from executive order.

Louis was no longer king, but as the living embodiment of the French monarchy remained a target for the republican revolutionaries. As such they engaged in a lengthy process of prosecuting him, first by taking up the question in the Convention whether it would be lawful to prosecute him at all for his actions as king, and as that passed after a lengthy debate, what kind of punishment he should recieve.

Despite there being a virtual civil war in France, and despite several massacres on royalists and nobles, most notably the September Massacres, it was still a huge deal to kill of the king himself. Opposition remained not just in the forces opposing the republicans but in Convention itself, and among the populace of Paris and the rest of France. So for the revolutionaries wanting kill of the French monarchy it was important to legitimise the process as much as possible, and as such they focused on a legal argument against the king in person and his actions in supporting various incidents where his guards killed civilians in the riots occurring in the early period of the revolution.

The debate on whether it was legal to prosecute the monarch became very technical and it did so with intent. With retrospective it can be questioned whether it was just to prosecute a king who had already been dethroned, and if so if it was legal to do so at the Convention instead of in a proper court of law. And these exact questions were voiced publically not just by the kings chosen defender but also by several members of the opposition in the Convent. And this is what underlines the fact of how crucial it was for the republicans to try and legitimise the proceedings as much as possible, because there wasn't 100% support in the convention itself, although there was a majority by far, for the proceedings and the execution. They succeeded and with that precedent they initiated similar process against the queen.

Sources: David P. Jordan, The King's Trial, University of California Press, 1979. Louis-François Jauffret, Histoire impartiale du procès de Louis XVI, 1793.