A few things to note about the study are:

• 40% of the women stopped the drug before the study was over.  In some studies up to 50% drop their hormone replacement therapy (hrt) within the first year.  Clearly, there is something to be learned about how to make hrt more tolerable.
• All of the women took the same dosage.  I don't know another medication with the potential dangers of estrogen where blood levels are not followed (when available).  With thyroid medication, we do not give everyone the same dosage.  Even with several different dosage forms of thyroid, even more elaborate dosing patterns are frequently used to obtain a blood level that is high enough to do the job and not so high to cause danger (therapeutic range).  I contacted the researchers and no estrogen levels are being reported yet.   Blood levels will be measured but the data is not available yet.
• The increased incidence of heart disease, stroke, and pulmonary embolus was not correlated to weight.  I don't think you would see this increased risk in these three events if the estrogen/progesterone combination was not given to the very obese.  Again, this data is not available yet but it could be that you do not see this increase in these diseases in those who practice a healthy lifestyle.
• This study used estrogen that is taken from a mare's urine (Premarin) and synthetic progesterone (Provera).  We have good evidence that estrogen and progesterone natural to a woman's body (available from compounding pharmacies) might not be as dangerous.  Some studies of estriol (another form of estrogen--Premarin is mostly estradiol) even seemed to show that the hormone protects a woman from breast cancer.
• If you want to read some of the study results for yourself and the opinion of the researchers you can go to the following sites:
• The actual JAMA   article
• Findings and implications according to the researchers who did the study.

When you've looked at things to be convinced that this study had it's problems (conclusions to be made still fuzzy), then go back to core article and read some good news about estrogen.