Probably not. It seems very unlikely.
I think Jewish people will mostly just be thought of as Westerners, and not particularly as Jews, even if they wear kippas, etc.
And in any case, India is quite a multicultural society with hundreds of various creeds and lots of religions. There is a longstanding tradition of being tolerant to other religions.
Well, I agree with Nikhil's comment that it would probably be somewhat unwise to walk around in a large-city Muslim neighborhood dressed in orthodox Jewish attire in the middle of the night. But that's a rather extreme example and even that would probably be alright most of the time.
The common mentality is: "We are happy to practice our traditions and keep our beliefs, and other religions/castes/groups are happy to practice theirs. Let's mind our own business while dealing in respectful, useful ways with other people."
Large numbers of Israelis and other Jewish people travel as tourists in India every year. I'm not aware of even a single case of religiously or ethnically motivated harassment. (If it occurred, it was probably just because they were foreigners, not in particular because they were Jewish. But note that Westerners are generally treated very well, so even that would not be a common or big problem.) Most Jewish people traveling in India probably don't wear kippas or otherwise look obviously Jewish, but I don't imagine it would be a problem even if they did. To be honest, I think they'd be treated pretty much like other Westerners. (Respectfully.)
I personally know an elderly Russian Jewish man who visits India every year, and he always wears a special Jewish hat (I don't know exactly what it's called, but I know it's not a kippa). I'm not aware that being Jewish has been a problem for him even a single time.
If you're worried about it, you can avoid discussing religion and politics while you're in India. However, I think even this would mostly be fine. As long as one doesn't go around invasively preaching or getting into theological or political arguments, it should be absolutely fine. I see India as a very religiously tolerant country.
Frankly, I'd be slightly more concerned if you were a Muslim (even though India has a large Muslim population), but even that would mostly be totally fine.
Source: Having lived and traveled in India for five years and talked to many Jewish and Israeli tourists and expatriates about their experiences here.