Although the point in the comments about stringsAsFactors option is TRUE :-), the real problem in your specific case is that cbind is coercing your data into a matrix. In R, a matrix, by definition, can only have a single data type. All integer, numeric, character or factor. See the following code examples:

# stringsAsFactors = TRUE
# wrong because the factors are coerced as numeric.
d <- data.frame(
  chr = c("A", "B"),
  start = c(1, 2),
  stringsAsFactors = TRUE
)
cbind(d$chr, d$start)
     [,1] [,2]
[1,]    1    1
[2,]    2    2

# stringsAsFactors = FALSE
# wrong because the numbers are coerced as character.
d <- data.frame(
  chr = c("A", "B"),
  start = c(1, 2),
  stringsAsFactors = FALSE
)
cbind(d$chr, d$start)
     [,1] [,2]
[1,] "A"  "1" 
[2,] "B"  "2"

So, if you use cbind, no matter how you set stringsAsFactors originally or whether you use readr or any other tool to read your data you screw, because a matrix can only have one type of data and you have two. The solution is to use a data.frame, which can handle different data types:

data.frame(chr2 = d$chr, start2 = d$start)
  chr2 start2
1    A      1
2    B      2

Don't forget to set stringsAsFactors as desired.

EDIT:

Note that cbind is doing this because you are passing two vectors. If you pass them as data.frame, cbind treats them as such and this problem is avoided:

cbind(d[, "chr", drop = FALSE], d[, "start", drop = FALSE])
  chr start
1   A     1
2   B     2

Of course, this solution is a lot more verbose.

This is a benefit of using the readr package rather than base R when reading tables, the stringsAsFactors option (this is what you were looking for) is set in a more coherent way.

The correct way -- and by correct, I mean correct: to specify with complete precision -- to solve this is to use colClasses with read.table, which coerces columns into type classes, like character, numeric, factor, etc.

For instance, in your case:

read.table(someFile, ..., colClasses=c("character", "numeric", "numeric"))

See ?read.table for more information.