Why would you need pybedtools? Just subtract the stop and start coordinates to get the sequence length. Put the lengths into an array and plot a histogram (or do whatever else you want with the lengths):

#!/usr/bin/env python

import numpy as np
import matplotlib.pyplot as plt
import sys

lengths = []
for line in sys.stdin:
    elems = line.rstrip().split('\t')
    lengths.append(int(elems[2]) - int(elems[1]))

plt.hist(np.array(lengths), bins='auto')  # arguments are passed to np.histogram
plt.title("Sequence lengths histogram")
plt.show()

To use, e.g.:

$ python ./so471158.py < in.bed