It shouldn't take much thought to understand that there is a difference between saying "there are many paths to Heaven" and "we should tolerate those who aren't on the path to Heaven". However, a common problem we experience in our fallen world is that things which shouldn't require much thought actually do. This is especially the case when it isn't something sinners want to think about.
In the modern world, "tolerance" has become synonymous with acceptance. If you "tolerate" someone, it is almost identical to accepting their beliefs. At the very least, you act as if those beliefs were somehow valid. By contrast, "intolerance" can be as simple as professing the truth that there is only one way to Heaven: Repent, and put your faith in the finished work of the Lord Jesus Christ through His death and resurrection. It does not need to be said to any Christian that this version of "tolerance" is really just the world's way of showing their own intolerance towards our God, and by extension, to His people.
But the actual meaning of tolerance is the ability to peacefully co-exist with people who differ from us in some way. As Christians, this is exactly what we are called to do. We may not agree with, or even like, the beliefs and practices of other people's religions, but we are called to live at peace with everyone. "Love your neighbour", "love your enemies", and especially "pray for those who persecute you", are not commands that extend only so far as the Church is concerned. It's not a case of "this enemy is a Christian, so you must love him, but this enemy is a Muslim, so feel free to shout bigoted slurs without the slightest provocation". You won't find this attitude in the Bible.
What you will find is multiple commands to extend love and grace even to those who don't believe. Sometimes, the reason given is even so they might believe. If you're tolerant to an unbeliever and they still call you "hateful" for preaching the truth, what can be said against you? You loved them as Christ, they hated you as Satan, they perished, and on their own head be it. But what if those accusations of bigotry are true? What if you not only hate unbelievers, but you show it too? And as a result, that is the impression of Christ you give them? If that happens, their blood is at least partially on your hands. You gave them reason not to come to the truth.
And so you see that the two original statements, while they are not the same, are actually linked. Because no, there are not many paths to Heaven, there is only one. But if we are intolerant to those who aren't on it, they have even less motive to get on it. Let us therefore be like Christ, living at peace with everyone, so far as that depends on us. Only when we are out of cheeks to turn should we lose even the slightest measure of tolerance.