While Mr. Braxton Bragg Underwood has not disguised his dislike for black people, and surely disapproves of Atticus's intention to actually defend Tom Robinson, he is, nevertheless, part of the business community of Maycomb along with Atticus Finch. And, despite his beliefs about segregation, he is probably fairly civic-minded and civilized; therefore, he would not approve of such lawless behavior as that planned by the Old Sarum Bunch.
Mr. Underwood illustrates that the belief in segregation is more complicated than simply "for" or "against" blacks. While he does not approve of racial mixing whether physical or social, Underwood does not believe in lawlessness and cruelty or blatant murder. Therefore, he would certainly want to ensure that Atticus's life is not endangered. Moreover, he would not want Tom so cruelly taken and killed. When Atticus tells Tom that the men are gone and he can stop worrying, Mr. Underwood chimes in,
"You're damn tootin' they won't. Had you covered all the time, Atticus."
While he believes in Jim Crow, it is not lawlessness that Mr. Underwood approves. So, he guards Atticus and Tom in order that no harm come to them.