The first thing I notice is that you need to find a better angle for the composition. The colors themselves, even from the point and shoot, if shot in raw (and with less noise) could be pretty easily salvaged by color grading. No amount of editing is going to solve composition and artifact issues though and the sample has issues with both.
Try to give things a more even and visually pleasing spread around the frame. You have a counter kind of sticking out from the side, just enough that you can't ignore it, but not enough to give a feel of it. You also have a large grey gap of floor running through the middle of the image. Possibly try to position it so that you have tables more evenly spread throughout the image (but at different depths). Also, pay attention to the angles of how the ceiling and floor are oriented in relation to the walls and any corners that are in the shot to ensure they appear to make natural looking angles. Currently, the camera feels like it is tilted a little clockwise (from the photographer's perspective) and the angle of the corner makes the room feel very narrow and long. I'd probably try a photo a little from the right of where the camera currently is in the sample and maybe down a little, to put the square back table more in-between the other two tables, but I'm not sure that would be the best shot. (The counter would likely still be troublesome.) Unfortunately without a better idea of the layout and scale, it's hard for me to give a better answer towards the sample photo in particular.
Whatever you do, be sure to shoot raw, particularly if you are trying to feature the lights and ceiling in shot. HDR and/or RAW highlight recovery should allow you to pull detail of the ceiling without compromising the rest of the scene. If you don't specifically want to include the ceiling, then don't. The large bright direct lights are going to detract from the intimacy of the scene that you generally want in a cafe/coffee shop atmosphere. The lighting should speak for itself in the way it lights the scene. It will also reduce lens flare issues if you continue to have flaring issues with your DSLR.
Other ideas that are more of a radical departure from your initial approach, try shots that capture the atmosphere as a cafe instead of necessarily just the details of the room. I understand that you are wanting to have an image to showcase your design of the space, but you design a space to give atmosphere, so don't be afraid to capture the atmosphere that it creates even at the expense of some detail. For example, I would probably try for a shot with some people sitting at a table, drinking coffee with a shot that features the product and shows the people enjoying it in the atmosphere. Have some shots of the room too, but if you're trying to sell yourself to a coffee shop owner, they're going to get far more excited by a shot that screams, intimate, classy spot to enjoy a good coffee than a sterile, empty (if colorful) shot of a mostly empty room. I'll see if I can find some examples of shots I took while trying to capture the atmosphere of the dining hall on my first cruise and post them as examples later.
Update: Ok, here are the samples I was thinking of though they aren't quite like I remembered them (these are from almost 5 years ago.) In the first, you can see the general setting clearly in the background, but the shot still has a defined subject.
This one goes in closer to the detail of the setting and is less personal, but gives a nice feel of the background and atmosphere close to the table.
This one is actually a different part of the ship, but focuses more on the layout of the serving area. You can see how it uses the angle between the two lines to make sure there isn't a wide gap in between, but rather makes it have a more intimate feel despite the fact there is actually a distance of probably about 20 feet between the two lines.
This is more of a detail shot that focused on a particular feature of the setting that I found particularly interesting. By altering the angle some, it would be easy for you to do something similar if there are any features that could be a subject of a photo unto themselves, but still show the background. For example, in this photo, if I was trying to show more of the room, I'd pull back and bring more of the room off to the right in to the frame.
This one allowed for a little more background that shows the overall feel of the dining room, though it's actually a sculpture that is outside the dining hall. I'd also go a fair bit wider on this shot if I was trying to feature the dining hall more prominently, though this photo was in particular trying to capture the sculpture.