A flogger has several "falls" or tails where, generally, a whip has one or two...or up to 6. There really isn't a consensus on what the difference is. Some say a flogger's falls are flat while a whip has braided or round falls. This would make a flogger "thud" and a whip "sting".

Personally, I call a flogger an implement with many falls, over 8-9, that are flat and deliver a thudding sensation. Rope floggers with many falls I lump in this category.
A whip has fewer falls or rounded falls that deliver a sting, whip score, and are not at all thuddy. The falls can be braided on a whip.

Confusing enough? The terms seem to be pretty common and interchangeable, it kinda runs to personal preference as far as I have seen.