הא דכרכים והא דכפרים ודכרכים אין מטמא בנגעים והתניא אחוזתכם אחוזתכם מטמאה בנגעים ואין ירושלים מטמאה בנגעים אמר ר' יהודה אני לא שמעתי אלא מקום מקדש בלבד הא בתי כנסיות ובתי מדרשות מטמאין בנגעים ואע"ג דכרכים נינהו אימא אמר רבי יהודה אני לא שמעתי אלא מקום מקודש בלבד
I'm having difficulty understanding how the גמרא actually answers the question here. The subject here is the גמרא's suggestion that the rural shuls may be subject to נגעים whereas urban shuls may not. So we directly question the assertion regarding urban shuls. The implication of the ברייתא is that any edifice at least outside of ירושלים may be subject to נגעים. So in the end, we understand רבי יהודה to mean that any מקום מקודש would be exempt. But then doesn't that exempt all shuls? How does this solve our problem. Yes, we have found an exemption for the urban shuls but we have not found a source to differentiate between urban and rural shuls whatsoever. Now, in truth, the גמרא eventually discards this approach for a similar reason later on. But couldn't they have done so already at this point?
I understood the answer to be specific to shuls in Yerushalayim (as the subject of the Baraisa is limited to that city) - the inference being that all shuls in other urban cities are still subject to Negaim.
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