Whenever I use the Sine Syntheziser, Instead of making a Sine Synth sound, It makes a flute sound.

Hi.

What were you expecting? The flute is basically the epitome of sine waves. I haven't listened to the soundfont you are referencing, but I would expect it to sound very much like a flute. :)

I'm sure if I'm wrong, someone will let me know. :)

I, too, use the MS Basic Soundfont and agree that the Sine Synthesizer produces questionable sound. To me it sounds like an ocarina (listen especially for each note's attack), and so I have prepared a demonstration of flute, sine synth, and ocarina.
Have a listen to this:
MS Basic soundfont.mscz
I exported it as a wav file and compared the waveforms of the sine synth and the ocarina. They were virtually identical - with negligible differences.

While it is true that flute produces a sound close to a true sign wave:

The difference is audibly discernable (think TV audio test signal vs flute).

So, if you wish the Sine Synthesizer notes to sound as sine waves (and not ocarina), see:
https://community.masteringmusescore.com/c/resources/ms-basic-individua…
which basically lets you select individual sounds to assign to an instrument -- as was possible in MuseScore 3.
So, you can download the file available there and choose 'Sine Wave' for the Sine Synthesizer.