Ive pondered this question myself on several occasions and have some possible hypotheses:
1. unfounded pre-conceptions.
As you probably know, FL studio started out as Fruity Loops. This was a very basic step sequencer which could load samples and manipulate time and pitch, and appart from some (terribly sounding) filters and sound shaping tools, that was it. It was considered as a bit of a toy. People who have no clue got stuck with that impression, ignoring how it developed from that into one of the most versatile, spontaneous composition tools today - IMHO.
other possible theories:
1. The name sounds very unimposing (compare "fruity loops" as opposed to the ring of say, "Digidesign Pro-Tools TDM", or "MOTU Digital Performer")
2. The interface design is admittedly, (but not unfortunately), a bit "cartoon" or "video game" like, if you know what i mean.
3. It is not associated with big studios or as an "industry standard" workstation. Therefore its assumed a toy for kids and amateurs who fill their time doing simple loops on their laptop whilst sitting on the loo or whatever.
4. its PC - only. this simple fact alone serves to discredit it by a big part of the "audio production population" who think that only macs are up to the job of using audio professionally.
Ive been producing music for almost 20 years and professionally for around 10, and have used every DAW that i know of. ive created some of my best music using FL.
Now as far as: what does cubase have that the other one doesnt? They are designed with a different approach to working. And they both have functions that the other doesnt. Thats why you use both Cubase AND fl studio, no?
it does not mean there are no workarounds, and certainly not than the one is better than the other.
All of the above are just personal opinions, but people who judge the quality of your results by the means with which they were created, absolutely miss the point, are probably ignorant, prejudiced, and not worth listening to.
To repeat what is being said over and over here, and which i totally agree with: its the musician that makes the music, not the tools he uses.
Sorry, rant over. touchy subject you see.