how does MFP come up with daily goals?

I shoot for over 100g of protein and 25g of fiber daily.

There is absolutely no reason why you shouldn't go over your fiber. I actually try to go over my fiber every day. Same goes with protein and healthy fats. Don't worry about those. Just because those numbers are red, doesn't mean they're bad!

If it bothers you, keep track of things like sodium instead. I try to keep that low.

It's fine to go over in protein and fiber! Fat try not to go over too much, although you should definitely try to meet the goal (not be too far under) using good fats.

I understand eating 1200 calories per day, but I'm finding it hard to even reach that amount without going over my max in the various nutrient categories, especially for fat, fiber and protein. My MFP daily goals are
fat: 40
protein: 45
fiber: 14 (!)

I haven't had dinner yet and already am over for fiber (14g seems really low!)

I know I can change the individual levels, but how do I know what to change them to??

Those are minimum goals for the things that have no negative effect, like fiber. Sodium is max limit usually.

Carb, protein, fat is FDA suggested levels for 2000 calorie diet.

Protein can always be gone over the limited amount they use, and as long as you get some good fats, the trade there doesn't matter.

Do some research on Google from respected sites, and make sure the perspective is of eating in a deficit.

Level correct for eating 2000 calories for maintenance may be too low when eating at deficit, where more protein is really needed.

Fiber doesn't affect your calorie count, but it does help to keep you full and satisfied, and cleans your system. Carbs, protein and fat make up the calories you are eating every day. Protein and carbs both have 4 calories per gram, fat has 9 (alcohol has 7 calories per gram but there isn't an RDA for it). The details for fiber and other micronutrients (i.e. vitamins) are guidelines based on the US RDA. Unless you have a medical condition a balanced diet should provide the necessary nutrition.

MFP uses the US standards to determine the base level of c/p/f for a 2000 calorie diet. As mentioned above the ratio can be changed. You'll get almost as many opions on this topic as there are MFP members.

Thanks for the info. I too was wondering about how they decide on the macro numbers for my 1200 calories. I usually go over in some area or another, but I'm not really counting anything regularly.