How were scientists and mathematicians in France treated during the French Revolution?

I have not studied the subject in detail but, in general, French mathematicians fared rather well under the Revolution. People like Laplace, Lagrange, Fourier, Monge, Legendre, Cassini., all had part of their most productive years between 1793 and 1815. Indeed, many held public or political offices.

Lagrange was from Turin, and as such got into some trouble around 1793 when the Convention issued decrees against foreigners who might be suspected of being hostile to the Revolution. However his friends were able to use their connections to keep him in France and safe. He was president of the Commission des Poids et Mesures for standardization of measurement units. In general, he did not show much interest in politics. He expressed regret at Lavoisier's execution, while on the other hand being sympathetic to some of the self-determination ideals of the revolution.

Fourier and Monge were enthusiastic about the Revolution, and held various political offices (among which Minister of the Navy for Monge and préfet of the Isère department for Fourier), and followed Napoleon to Egypt.

Napoleon himself was quite enthusiastic about mathematics. The jury is still out on what exactly is his contribution or connection to Napoleon's theorem, but he was generally interested by the subject, and had great admiration for the mathematical giants of his time. Mascheroni dedicated his book on compass constructions to him, and Laplace dedicated his Celestial Mechanics to Bonaparte (he removed the dedication from later editions after 1815).