Try temporarily disabling all rules (un-check them) and see if it still trashes your mail when you get new hotmail.
If it no longer trashes your mail then it was a mail rule.
If it still trashes your mail then it's the junk mail filter. Lower the threshold in your Junk E-mail Protection settings.
If it seems to be a mail rule, pull some of the hotmail messages from the trash and put them in your in-box. Then activate a couple of rules at a time, select the hotmail messages and choose Apply Rule: All Rules to the messages to see if one that you've just activated is the culprit. Continue on in this fashion until you find the problem-rule.
Just speculation, but have you recently renamed or deleted a mail folder? Because mail rules link to the folder by ID, not by name, even though you see the name in the Rule settings. So if you've been messing with your folder-hierarchy, it could throw off your mail rules pretty badly.