There are several classes of mutations in the CF gene that can be responsible for the malfunction in chloride conductance. These mutations disrupt CFTR function in the following ways: preventing expression of the transcript, reducing cell-surface expression of CFTR, impairing channel regulation, or by altering the channel properties. However in 70% of cases, the mutation is a three-nucleotide deletion which eliminates the amino acid phenylalanine from the protein CFTR, and because of the location of the absence, CFTR does not fold properly and cannot leave the endoplasmic reticulum/Golgi system.
As a consequence of these changes, chloride ions (negatively charged) that usually move passively through the CFTR and maintain equilibrium between the intracellular and extracellular space, now become trapped inside the cell. This in turn disrupts the electrical gradient, so that sodium ions (with their positive charges) also do not have their usual concentrations inside and outside the cell (sodium now stays inside the cell). Since NaCl becomes trapped inside the cell, water also moves from the extracellular space into the cell by osmosis, resulting in the accumulation of a higher than normal concentration of salt outside of the cell - the basis for the sweat test for cystic fibrosis (patients have higher than normal concentrations of salt in their sweat).
Due to this accumulation and the lack of normal water transport, the fluid layer in the lungs becomes more viscous and contains a higher concentration of mucous than in normal patients. The mucous plugs impair breathing and trap bacteria, making infection more likely. Additionally, the high NaCl concentration of the surface fluid in the lungs inactivates the antibacterial agents secreted by the lung epithelial cells. The bacteria therefore multiply, and most CF patients have established chronic pulmonary infection within the first few months of life. The resulting inflammatory response contributes to the mucous and leads to chronic lung damage.
So see how much trouble a little thing like negatively charged chloride ions not being able to move out of your cells can cause?? I hated taking a course on ion channels my first-year in grad school (I'm a behavioral neuroscientist, and had had all the electrical engineering I wanted in college), but the darn things are actually very important.
Information taken from Ion Channels and Disease (2002) by Frances M. Ashcroft. Graphic and description can be found here.