There are different degrees of separation, as outlined in the article. As to why:
1. As I said the focus is on local churches. Most of us believe in the universal Church(the Bride of Christ), however, we also believe Christ will carry out the the work through local churches and also that the emphasis of the New Testament is on local churches. There are some IFB churches that preach the "Baptist Brider" theology that teaches only Baptists are the Bride of Christ, but as said, all IFB churches are separate.
As IFB members, we don't believe in church conventions(such as the Southern Baptist Convention) and mission boards that dictate the local churches. We do, however, have alliances and fellowships, but those have no or little control over what each member church does. For example, the Southern Baptist Convention forced the use of the NIV Bibles and every member church had to follow suit. Not so with IFB churches. If one IFB church uses the NIV, no other church will be forced to go down that road.
2. Baptist throughout history have always been clamoring for separation. The first Baptists was always separate from the Catholic church(they are not Protestant, Protestants separated from the Catholic church. Baptists were always separate). Roger Williams, first Baptist in America, who founded Providence separated from Puritanism. Jack Hyles separated from the Southern Baptist Convention. Baptists are marked for their separation.
3. Can two walk together unless they be agreed? (Amos 3:3) As IFB members, we also apply this to believers, not only unbelievers.
4. To stem the tide of non-denominationalism. Most non-denominational churches were Baptist, who we think have compromised.
5. To stem the tide of ecumenicalism. Unification with other churches means compromise. Compromise prevents us to "worship Him in spirit and in truth."
This applies mostly on churches as a whole, not the individual members as much. For example, I am on this forum conversing with other Christians who are not the of the same mind as I am. I will pray for you, answer questions, help you, ask questions, as a brother in Christ, but I won't, at least I hope, compromise for the sake of unity.
Some IFB churches do this just to judge others and feel spiritual moral. But some do it so they can simply make it and because they love Jesus. I will not deny that there is no hypocrisy. Because there is. Some IFB churches are more balanced than others.
On a side note,
Have you heard about the Baptist Distinctives?
"Baptists may not order their distinctives the same but all would include those below as being those which are primary to their identity.
Use the B-A-P-T-I-S-T-S acrostic to familiarize yourself with them.
B Biblical Authority ~ 1st Thessalonians 2:13
A Autonomy of the Local Church ~ Colossians 1:18
P Priesthood of the Believers ~ 1 Peter 2:5
T Two Ordinances of the Church ~ 1 Corinthians 11:23-24
I Individual Soul Liberty ~ Romans 14:12
S Saved and Baptized Church Membership ~ Acts 2:41&47
T Two Offices of the Church ~ 1st Timothy 3:1-13
S Separation of Church and State ~ Romans 13:1-3"
taken from: http://www.allaboutbaptists.com/distinctives.html