I hope not to appear too stupid 
but could someone explain to me if there is a difference between the fingering of a whistle versus a flute? What key can a flute play in? Is it the same as a whistle? I feel so dumb asking this question. 
Never feel stupid for asking an honest question! 
They fingering is identical until you get to some of the half-holing/cross-fingering, and then they can become manufacturer specific (IMH - and very limited - O…). Check out the fingering charts at Fingering Charts For Keyless D Flutes | Martin Doyle Flutes
Simple wise guy answer: One is held out to the side and the other straight up and down. The inevitable condensation drips onto the whistle players own leg. The condensation from the flute falls on the banjo players leg next to them. They play the same notes with the same fingers.
More seriously though … The noise making mechanism is the big difference between what we call the Irish whistle and what we refer to as the Irish flute (I am talking keyless flutes here). Both are diatonic instruments. Both use the simple system for fingering each note. Both play two full octave at the minimum. Fewer whistles will play into the third octave but flutes will generally do better up there. Both play primarily two keys without gymnastics - the major scale in the key of the bell note and the major scale of the fourth note in the primary key. D whistles and D flutes are the standard keys. Both will also play in the key of G with one cross-fingered/half-holed note - the C natural note. The low D whistle plays the same notes and octaves as the D flute. You will see both instruments made in a variety of keys to accommodate playing with others in different keys. The flute however has from the 18th century used keys to play additional notes. Then in the 19th century all Hades broke loose until there were flutes with eight or more keys. So a fully keyed flute can play chromatically and therefor in any key required. But it is still a simple system flute albeit in wolf’s clothing. There are fully keyed whistles too, but they are not as common as keyed flutes.
Now playing the two is a totally different deal. The whistle is by far the easier of the two. Anyone can pucker up and blow. The flute takes some time to master and for many it can take a while to be able to generate a solid tone. To play the second octave on a whistle you just blow harder. On a flute you have to tighten the lips to accelerate the air jet to get the second octave. That’s a large difference between the two. The flute has a greater dynamic range in general. The flute also allows the player to shape their embouchure and vary the angle of the air jet to change the timbre of the notes. The flute is, believe it or not, the more efficient of the two in air usage. But a beginner will not think so as they pass out trying to play the high notes.
Of course once you master that stuff, the notes of the tunes are still fingered the same. Technique may differ quite a bit in ornamenting the tunes. But at the heart of it they are both simple system flutes.
The whistle is the cuter, more lovable instrument. The flute is the attractive, bad boy instrument.
Hope that helps some.
Feadoggie
Also, when you play the flute nobody will ask you (as many often do with the whistle) “So, is that a recorder?”
Unless you’re playing a timber flute to an audience who’ve only ever seen Boehm typewriters before, in which case there’ll nearly always be someone who asks ‘Is that a flute?’; and the same people just have no idea whatsoever what the low whistle is …
Thanks everyone for your great help. It was a question I thought was too dumb to ask. 
Feadoggie I loved your reply about the flute being a bad boy instrument. I like your style. 
Debbie
I finger both the same, as far as which fingers are lifted when, a Low D whistle and D flute producing exactly the same notes.
But the hand position or hand posture is completely different (in most cases).
There’s a variety of ways that trad Irish fluteplayers hold their flutes: some have both hands exactly as Boehm fluteplayers are taught, some have the upper hand the same as the Boehm flute but their lower hand with flat fingers (Matt Molloy, myself, and many others), some have flat fingers, the so-called “piper’s grip”, on both hands (in other words fingering the flute as if it was a Low Whistle).
On whistles likewise there are a number of different “grips” people use and it can vary, with the same player, depending on what size whistle is being played. So for myself I use four different “grips” whether I’m playing the flute, a high whistle, a low whistle, or an uilleann chanter.
No, they ask if it’s a clarinet. 