Immediately after his assassination, Marat is held to a quasi-saint role, with his bust/statue often times replacing crucifixes in churches. The port of Le Havre de Grace even renamed itself Le Havre de Marat, however after the Thermidorian Reaction, where Maximilien Robespierre is ousted, public opinion quickly flipped. His body was disinterred, people openly mocked him, and on numerous occasions artistic depictions of him were destroyed, yet I can't seem to find any information on why this occurred.
Marat was revered as a revolutionary saint after his death, as the Hébertistes took him to be a victim of the Gironde (Charlotte Corday was from Caen where they had fled and didn’t hide her sympathies for them). For the rising Jacobins, enforcing the cult of Marat was a way to channel the more radical elements of the Revolution, and they pushed for the Convention to admit his ashes to the Pantheon. Radical elements were important as the sans culottes were the ones asking for reforms, using force if necessary. The enragés, among them Hébert, were also very popular in the army where the Père Duchesne, Hébert’s newspaper, was wildly distributed. Robespierre wasn’t a big fan of the Sans Culotte or the war or even of persecuting the Girondins, and playing the Marat card was a cost-effective propaganda tool. His ashes were admitted to the Panthéon a year later in September (Vendémiaire) 1794.
After Thermidor and the fall of Robespierre, Marat continued to be revered, mostly as a journalist, as newspapers took the lead of the Thermidorian reaction, among them L’Ami du peuple - a title bearing Marat’s nickname -, but things changed quickly with the return of the Gironde. On December 9th 1794, the Girondins came back to the Convention. By the end of the month, remaining elements of the Jacobins who had been involved in the repression of the Vendée and of the Gironde, notably Collot d’Herbois and Billaud Varenne of the Comité de Salut Public, were prosecuted. Marat’s ashes were removed from the Panthéon on February 8th 1795 and buried quietly somewhere else.
What had changed ? Well, the reason for Marat to be introduced in the first place was that he could pose as a martyr when the Convention was facing two perils : the war abroad and the civil war. The streets had ended the Girondins reign about a month earlier, and both the radical Sans Culotte and Hébertistes were needed by the Jacobins to control some sort of government. In 1794, things had changed : the French army was now winning the war against all odds and the Convention was looking for peace in the Vendée and in Britanny; the Sans Culottes had fallen, the Hébertistes were gone... There was no need for such a polarizing figure, the Jacobins were footing the note for all the repression and the Gironde was back, wishing to avenge the humiliations of 1793. So off went the idol who had been forged only a few months prior, a testament to how quick the situation changed in the years 1793-1795.