Does it make any sense for the bridge to be a distinct module sitting right atop the ship? No, not really.
But, at the same time, were the bridge buried deep within the bowels of the ship, it wouldn't really make much difference. Shields are what keep the whole ship intact. Look at TUC. Once the shields are down, a single photon torpedo is able to rip through the entire saucer section from bottom to top. Wouldn't matter where the bridge is at that point. It would still be just as vulnerable.
Also, tactically speaking, why go after the bridge anyway? Just for the emotional punch of killing the captain? If Picard and the bridge crew get taken out, it's not as if the other 1,000 people on the ship would just surrender. Pretty sure everyone from LaForge in engineering to Ensign Ricky in stellar cartography would continue to fight.