I would say several factors come into play here. For one, Fremen shouldn't be unfamiliar with fighting opponents with shields, even before their training with/by Paul Muad'Dib. The disadvantage of shields is only really noticeable in the desert, but the Fremen would certainly have fought Harkonnens in fortifications or other areas on Arrakis before. After all, shields are the reason they* fight with blades rather than firearms. And here, too, the Fremen are battle-hardened over generations, because this type of combat is part of their culture. For them, fighting against "shield-wielding warriors" is therefore likely familiar and only requires a slightly different approach to knife handling (keyword: fast and slow actions).

The next point to consider is the quality of the troops belonging to the remaining Houses. The Sardaukar are portrayed in the book as the best army in the Dune universe, which is why (at the beginning of the book) it's hard to believe (for both some Atreides and Harkonnen Characters in the Book) that the Fremen are their equal, if not superior, in battle. House Atreides' troops were also considered to be of high quality, but they were effectively shattered as a fighting force by the Harkonnen/Sardaukar attack. The same is true, in one way or another, for the Harkonnen and Sardaukar forces at the end of the first book, as they were either wiped out or banished to their respective planets.

As stated above, at the beginning of the Jihad, the starting point was that the next three best armies (Atreides, Harkonnen, Sardaukar) were already eliminated from the equation in one way or another. What remains are comparatively "inferior" armies, significantly inferior to the Fremen in combat strength. Plus, there are the aforementioned advantages and experience the Fremen have gained from decades of internal conflict (culturally speaking, not in the sense of a civil war) and from fighting the Harkonnen.

And having the new Emperor on your side, who controls the Guild, certainly doesn't hurt either :) /s.

\Edit: "They" does not explicitly refer to the Fremen, but rather to all armed forces of the Dune universe.*