This is a really interesting question actually! I'm new to answering questions on this site but I'll explain as best I can.
As others have said, the difference in this particular calculation comes down to nuclear binding energy. As jimchmst pointed out, you can just look at the weights of the atoms to see this difference.
If you add up the mass of 6 protons and 6 neutrons, and then divide by the conversion factor from kg to amu, you get something around 12.096, but the actual measured mass of carbon-12 is exactly 12 amu.
This difference turns out to hold true for all nuclei; their mass is a little less than the sum of their parts. The reason for this is conservation of energy and the mass-energy equivalency. Nuclei are more stable together than apart (generally) - that is why atoms exist all over the place! This means there must be an energy difference between the protons and neutrons apart and the protons and neutrons together. But that energy that had to have gone somewhere - it was carried away as a high energy photon when the nucleus was made. Since mass and energy are equivalent, this means that some mass was also lost in the formation of the nucleus - the mass defect.
If you look up the masses of carbon-12 and oxygen-16, and add them up stoichiometrically for CO2, you get about 43.99 - very close to the true molar mass of CO2! The remaining difference comes from isotopic abundance - that is, not all carbons have 6 neutrons, and not all oxygens have 8.
For CO2, it works out that the isotopic abundance makes little difference, but for some other molecules this is not always the case. Take for example, HBr. Bromine has two main isotopes which are roughly equally abundant. Attempting to calculate the molar mass of HBr using either one of the isotopes' mass results in a molar mass off by almost 1 whole amu! The true molar mass is a weighted average of all the possible masses of each combination of isotopes. When calculating the molar mass of a compound, we generally start from the masses given on the periodic table because these already account for both mass defect and isotopic abundance.
Hope that helps!