Actually, no. "Inflammable" and "flammable" mean the same thing, reach back to the same roots, but were brought into English independently. "Inflammable" got to us first, and for a very long time "flammable" was viewed as a vulgar (as in "common" or "uneducated" rather than as "nasty") term; a sign of the decline and impending death of English as a civilized language.
The "in" prefix of "inflammable" is from the original French word (and related to the "in" and "im" prefixes indicating "taking in, especially of a quality", as in "imbued" and "imbibe"), and is not related to the negation prefix we borrowed from Latin. Unfortunately, the normal meaning of "in" as a prefix has led to some rather unfortunate misunderstandings (often fatal), so it is more common to see the word "flammable" used in product warnings and so on (whereas "inflammable" was once the much more common word of the two).