Why does meiotic recombination disrupt the independent assortment of genes on the same chromosome?
Recombination does not make any two genes completely independent because there will not systematically be a recombination event between two given loci (=position on the chromosome).

Distance between loci

Consider two scenarios that describe the position of two loci on a chromosome. 


Tightly linked loci


Consider two very closely linked loci. Let's say that a recombination event occurs somewhere in the chromosome. It is very likely for this recombination event to occur somewhere else than between these two loci. These two loci are essentially linked and do not segregate independently


Distant loci


Consider now two loci on the same chromosome. Each locus (=singular of loci) is found at one end of the chromosome. If a recombination event occurs, it is pretty sure that it will occurs between the two loci. As a consequence, the two loci will segregate (quasi) independently.

Conclusion

As a conclusion, recombination allows to break down the linkage between two loci but it does so at a given rate that depends on the physical distance between the two loci and on the per nucleotide recombination rate.