Visiting Jerusalem is up for debate now, and it's good that it is being taken up and understood now. The question is not whether to visit Jerusalem or not, rather it is visiting it under Israeli's occupation. Islamic scholars have different opinions on this, all of which are respected.
Let's look at it from the religious perspective first. Jerusalem has always been a sacred place as mentioned in the Holy Quran "... to Masjid Al-Aqsa, whose surroundings we have blessed..." (17:1). It is the land of prophets all of whom are revered and respected. This mosque is the place where all the prophets (May Allah be pleased with them all) met on the night of Isra. When the Holy prophet (PBUH) migrated to Madinah, the Muslims prayed in its direction for more than one and a half year. Being host to the third holiest place of Islam, Jerusalem is equally dear to Muslims, as it is for Jews and Christians. The holy Prophet (PBUH) has specifically mentioned Al-Aqsa Mosque to be visited along with the ones in Makkah and Madinah. So it's more important for Muslims to try and visit there if conditions allow. Though under Israeli occupation, we can still go there via Jordan. According to some scholars, it's like recognizing Israel, and they have a valid point too - in accepting the norms and procedures formed by the occupying Israeli government.
But let's look at the other side as well. All these decades we have been "not recognizing Israel", but have also been losing an opportunity to visit Al-Quds. So just by going there, do we "recognize Israel"? No, as long as you are just going to fulfill your religious duty. We have the treaty of Hudaibiyah as an example, where the holy Kaabah was still in control of the Quraysh, but the Prophet (PBUH) and his companions made a pact with them, stayed in Makkah for three days and performed their pilgrimage. Did they recognize the Quraysh's ownership of the Kaabah? Definitely not.
Babri Masjid as it stood once in India
Now coming to the political and strategic aspect - Israel has long been trying to drive out all the Palestinians from the remaining lands they hold. And it has been blocking all attempts to even talk of return of refugees to their own country. The only aim is to declare and let the whole world accept Israel as a Jewish state. More importantly there have been concerted efforts to Judaize the surroundings of the Al-Aqsa Mosque. Now if Muslims continue to isolate Jerusalem and Al-Quds, just because its under Israel, will it not boost their efforts to Judaize the whole of Jerusalem? The more number of Muslims visiting Al-Aqsa, the more Islamic right it retains. Of course, the struggle against the Israeli occupation can continue, but the more we shun Jerusalem the stronger will be the Judaization of Jerusalem. If we are honest with ourselves and with the Palestinians, we really don't see even a rare chance of Israel returning back the occupied territories in decades to come. So how long will we be leaving Jerusalem alone? And what do we say about the Muslim countries who already have either full diplomatic ties with Israel or have some tacit (hand in glove) understanding with Israel? Refrain from them as well?
An interesting example should be of significance here: The destruction of historic Babri Masjid in India at the hands of right wing Hindu fanatics. The controversy and court cases over this issue were in existence ever since the British rule in India. At one time a court declared the complex locked for both Hindus and Muslims. And after decades the locks were opened and Hindus given access to perform their worship, thereby reducing the Muslims' chances of winning back the right to offer prayers in the Masjid. One of the significant stands taken by right wing propaganda in the run up to opening the locks for Hindus was - "No Muslim prayers were offered there for so many decades, No Muslim ever entered there so it cannot be a Masjid".
