Why is the 3'UTR region highly methylated in most of the human genes?
According to Choi et al. Genome Biology 2009, 10:R89, DNA methylation at both coding boundaries may regulate transcription elongation and stabilize splicing by reducing the occurrences of exon skipping.

From the abstract:


  Here we report a genome-wide observation of distinct peaks of
  nucleosomes and methylation at both ends of a protein coding unit.
  Elongating polymerases tend to pause near both coding ends immediately
  upstream of the epigenetic peaks, causing a significant reduction in
  elongation efficiency. Conserved features in underlying protein coding
  sequences seem to dictate their evolutionary conservation across
  multiple species. The nucleosomal and methylation marks are commonly
  associated with high sequence-encoded DNA-bending propensity but
  differentially with CpG density. As the gene grows longer, the
  epigenetic codes seem to be shifted from variable inner sequences
  toward boundary regions, rendering the peaks more prominent in higher
  organisms.


Their data (figures 1 and S2), however, do not support a generalized increase in the 3' UTR regions in either human T cells, mouse liver, yeast or flies.