Conversely, mic it right and choose the right place to record, and if you know your tool, you can create awesome recordings. Record with a crappy mic that's not been properly placed in a room that's not properly soundproofed, and Bob Katz himself couldn't fix it. Professionalism comes from a.) the recording quality and b.) the skill of the engineer. The tool, in and of itself, it not the issue. There are going to be inherent differences in the audio codecs depending on which one ships with whose products. ProTools can't make better ones or zeros than any other package. That's a huge plus in terms of learning curve for getting things done.
Let's start with this: FLStudio it's a tool with which you're familiar. See this related question - it's about the video production's vibe that Sony Vegas in 'unprofessional' compared to Avid (who make ProTools) and Final Cut.
