Should I see a specialist for wegener's granulomatosis, or can my regular doctor take care of it?

Uncommon problems. ...Like wegener's require someone with experience to manage all the myriad manifestations and potential problems (how's that for alliteration) that can come with the disease or its treatment. Its possible but unlikely that your regular doctor has such experience, if i had wegener's i would be looking to at least have my doctor consult with someone who sees this problem frequently.
If experienced w/it. If your doc has ample experience with this uncommon disease, then yes. However, it may be in your best interest to seek out the opinion of specialists who have had ample experience, whether a pulmonary doc, ent, kidney specialist (nephrologist), hematologist (blood specialist), and/or immunologist, depending on the severity of the disorder. Any/all should work with your doc.
Specialist consult. Since untreated Wegener's is fatal, and since the meds are very powerful and can have some nasty side effects, you'll do best to get at least a specialist review before initiating treatment.
If needed. Your primary care physician may be managing your disease well. However, if you are having constant flare-ups of lung and/or kidney diseases, along with upper airway exacerbations, you may want to consider adding a nephrologist and/or pulmonologist to your treatment care. If your disease is well-managed then a specialist should not be necessary.